There are two ways i can think of, the first one would be to create an ani ( eff ) file, and each two files are dark, means no glowmaps ( 2 frames glowmap, then 2 frames a dark bitmap then 2 frames glowmap aso ).
The second way use the deactivate glowmaps / activate glowmaps SEXPs, with a delay of 1 second.
If the vessel is damaged when the player arrives you could make
has-arrived-delay ( other triggers are probably better )
--------0
--------Alpha1
-----deactivate-glowmaps
------------<the name of your ship>
then make a similar event which activates the glowmaps, chain 'em with a high repeat count.