I can't imagine what could be causing ships to become invincible the way you describe, particularly if you're using a ship-vulnerable SEXP on all of them. Do you know what version of FRED2 you are using, or what build of the SCP you use to run TBP/FS2? Just for troubleshooting purposes, you might try making an event that lists all the ships in the mission under ship-vulnerable and give this event a repeat count of 999 and a repeat interval of 1 second. If that solves anything it might indicate the problem is scripting related as opposed to some weird hickup in the code.
Unless this has been changed by the SCP, Red Alert specs will only get carried over from mission to mission if they've already been linked together in a campaign. If you play Mission 1 as a single mission and Ship A has 56% hull integrity, Ship A will likely have 100% hull integrity in Mission 2, even if its flagged for Red Alert Carry Status.
If you are playing these missions in campaign mode, make sure the names of the ships in a mission (and all subsequent missions where this applies) that you want to retain damage have the same exact name as they did in the previous mission(s). And though you've probably already done it, make sure the Red Alert Carry Status flag is checked for the ships you want to carry over, and that "Red Alert Mission" is checked under the Mission Specs Editor (unless this has been changed by the SCP people).
Understand that you may have set it up right, but if you're playing these missions as single missions (from the Tech Room), you're not going to see the results yet. As far as I know, the game does not keep variables stored from one single mission play session to another. Once you've got your missions linked together in a campaign, you should see what you're looking for.
Variables can be a substitute for this; scroll past the next section for an explanation.
CommAnis have to be entered manually the first time you use them in a mission because the ones in the drop down menu, long story short, are basically incorrect. Input any of these to get what you want:
capcomm_1_MINBARI.ani <<< female Minbari of the warrior caste
capcomm_2_MINBARI.ani <<< male Minbari of the warrior caste
capcomm_CENTAURI.ani <<< male Centauri official
capcomm_Corwin.ani <<< Lt. Corwin of Babylon 5
capcomm_DRAKH.ani <<< a Drakh
capcomm_Delenn.ani <<< Delenn in her post-Revelations look
capcomm_EA.ani <<< Capt. Ellis Pierce of the EAS Hyperion
capcomm_Garibaldi.ani <<< Garibaldi in civilian clothes
capcomm_Hague.ani <<< Gen. Hague in dress uniform
capcomm_Hall.ani <<< Capt. Hall of the EAS Heracles
capcomm_Hiroshi.ani <<< Capt. Hiroshi of the EAS Churchill
capcomm_Ivanova.ani <<< Cmdr. Ivanova in Army of Light uniform
capcomm_James.ani <<< Capt. James of the EAS Agamemnon
capcomm_Lefcourt.ani <<< Gen. Lefcourt on bridge of the EAS Apollo
capcomm_MacDougan.ani <<< Capt. MacDougan of the EAS Vesta
capcomm_MacDougan_2.ani <<< Capt. MacDougan sitting in his chair, not talking (?!?)
capcomm_Mollari.ani <<< Ambassador Londo Mollari staring idly at the camera (...)
capcomm_Morden.ani <<< Mr. Morden talking
capcomm_NARN.ani <<< male Narn speaking
capcomm_Ryan.ani <<< Maj. Ryan of the EAS Alexander
capcomm_Sheridan.ani <<< Capt. Sheridan in Army of Light uniform
capcomm_Vorlon.ani <<< a Vorlon
pilot_CENTAURI.ani <<< lower ranking male Centauri
pilot_DRAZI.ani <<< Drazi pilot
pilot_EA.ani <<< male Starfury pilot
pilot_EA_2.ani <<< another male Starfury pilot
pilot_EA_Clarke.ani <<< EA pilot in Thunderbolt cockpit
pilot_EA_dying.ani <<< EA pilot losing control, followed by loss of signal
pilot_EAservicecraft.ani <<< Construction Fury pilot
pilot_EAservicecraft_dying.ani <<< Construction Fury pilot buying the farm
pilot_Gkar.ani <<< Ambassador G'Kar in a fighter cockpit
pilot_Garibaldi.ani <<< Garibaldi in a Starfury cockpit
pilot_MINBARI.ani <<< male Minbari inside Nial
pilot_NARN.ani <<< male Narn in fighter cockpit
pilot_RAIDERS.ani <<< male human in Zephyr cockpit
Note that the .ani file extension must be included when you type these in if you want to see them show up in mission. Also note that once you've typed them in manually and closed the event editor, you do not need to type them in again as they will be saved in the mission file. For instance, if you type in "pilot_RAIDERS.ani" for a message's comm animation and close the Events Editor, save the mission, and reopen the Events Editor, you will be able to pull down "pilot_RAIDERS.ani" from the drop down menu.
With the advent of persistent variables, maintaining damage consistency from one mission to the next without using the Red Alert flags should be a possibility. Generally speaking, using these variables will be messier than getting the Red Alert method to work. You will need an individual variable for each factor you intend to keep in one mission. For instance, if you want to carry Ship A's hull integrity from Mission 1 to Mission 2, you will need an event that defines a variable as Ship A's hull integrity at the end of that mission. Here's an example event:
Check Harrisburg Integrity
--when
------has-time-elapsed
---------15
------modify-variable
---------HarrisburgHull(0)
--------------+
-----------------hits-left
---------------------EAS Harrisburg
-----------------HarrisburgHull(0)
The variable here is "HarrisburgHull." It's important to remember that it's default value is zero. This example event would add the Harrisburg's hull integrity percentage to the variable 15 seconds into the mission. So if after 15 seconds the Harrisburg has 100% hull integrity, the event will add a value of 100 to the variable. You can change the "has-time-elapsed" part to whatever works for the mission you have in mind; whatever you do, you'll want to collect the ship's specs only after they won't be changed (i.e. it's about to jump out). Make sure when you create the variable in the Events Editor you check the "Campaign Persistent" box so it can carry over from mission to mission. In the next mission, you would need to set up an event like this:
Set Harrisburg Integrity
--when
-------has-arrived-delay
-----------EAS Harrisburg
-----------0
-------set-subsystem-strength
-----------EAS Harrisburg
-----------Hull
-----------HarrisburgHull(0)
This event will set the Harrisburg's hull integrity at whatever percent is defined by the variable here. Since the variable holds the value of the Harrisburg's hull integrity from the previous mission, the two should remain consistent.
Note that you'll need to recreate the variable you used from the last mission in the new one, character for character, so that when the game looks in the campaign file for it a match can be found.
Now the reason I say this method might be messier is because the more specific you want to get with it the more work you'll have to do. For instance, if you want to carry over the damage from the Harrisburg's subsystems, you'll need an individual variable for each of them. The same goes for turrets. Also, because variables aren't kept from a single mission after you exit, you won't see the desired results doing this either unless you're playing the missions in a campaign. As a matter of fact, were you to use this example in a single mission, this method would destroy the Harrisburg upon its arrival in the second mission since the default value of the variable implemented is zero (kaboooom). In other words, don't use this method and test your missions outside of a campaign as results will be worse than before. A workaround to this problem exists where you could create an event that boosts the variable's value if it turns out to be zero at the beginning of the mission (which it will be if it's being played as a single mission). Doing that might create a new plethora of issues which I won't get into unless you want.
Basically, the Red Alert method can save time here. If you're playing your missions as a campaign and you think it's set up right and it's still not working, you might try this or ask/search for help on the SCP forum. If you're playing your missions from the Tech Room, however, don't worry. The Red Alert thing doesn't really work there because it's not supposed to work there.
Sooner or later someone with a more evolved sense of communication will come along and explain this stuff more eloquently, so don't worry if you didn't get it.
You may also try posting in the
FreeSpace Campaigns forum. Those guys actually stay on top of SCP developments and know the ins-and-outs of getting SCP enhanced FRED2 elements to work.