I now have my build settings set to "Nightlies" and when I try to direct my mod's FSO tab to that build, it first allows it, then when I try to upload, it says I can't use a local build. Of course I do have it installed, otherwise I wouldn't be able to point the "Browse" window to that .exe file. I still have the same three builds listed: 19.0.0, the december 11, 2020 nightly and the 21.0.0. I assume they're the requirements of the mods I have installed via Knossos.
By overriding it, I mean I had the original RR_v144.vp uploaded with the RC2 features at first (night of April 13), then changed some files to remove the post-21.0.0 features (changed four or five missions), recompiled the RR_v144.vp, then tried to get Knossos to change its version of RR_v144.vp to the new one (morning of April 14). When I tried to point my updated VP to it by clicking on the folder path below "Mod Path", it opened up a browser where if I double-click on a .vp, it opens up QuickVP as opposed to recognizing it as the new version I want to override the old version with.
Note: I'm developing from the traditional Games/FreeSpace 2 folder and using wxLauncher. Those few mods I have via Knossos are in Games/FreeSpace 2/Knossos. I haven't had a version of RR in my Knossos folder until I tried the version I uploaded following the "error" report about mission 4.
Also despite apparently deleting the mod, I was still able to re-download it from the Explore tab to check if your advice about Preference settings work.
From the previous post, I forgot to mention that my plan in deleting was to first delete the whole mod entirely, then upload the same thing again with the same settings and same steps (now with the RR_v144.vp I'm using as the base .vp being from the morning of April 14) to preserve the original link to Knossos in the OP by using the same ID, I wanted to avoid the confusion of having three version of RR available (the first one being Novachen's revision of an older version, the second one being the original release with 21.2.0 features, the third one with the 21.0.0 "updates").
[EDIT2]Hang on a second.
I just started the current version from Knossos and for some reason it ran the 21.2.0 RC2 build with it, and mission 4 loaded without a problem. I still don't have the 21.2.0 RC2 build in FreeSpace 2/Knossos/bin - it's in the root FreeSpace 2. Maybe it did recognize the RC2 build but the software believed it didn't and sent the error message instead? I have no idea what happened.