Even if they can't convert pre jump, couldn't they just have the converted ship teleport to your capital(or if possible the planet it fled) after it finishes it's jump?
Doesn't make a ton of thematic sense, but accomplishes pretty much the same thing as having it converted pre-jump.
Also, when you're at max fleet supply it should at least destroy fleeing enemy frigates even if it can't convert them.
Personally though, my preference would be to just buff the numbers rather then doing anything to protect the ships- sure you're unlikely to actually keep the ships unless you give chase with your fleet(don't give them time to kill the converts before the pursueing fleet jumps in)- but we need to ask ourselves- what Is the role of this tech strategically.
The role first and foremost is that the ability makes it so if the enemy tries to bypass frontline planets or is forced to retreat from attacks too often, they grow weaker relative to their opponent as each jump converts a portion of their fleet. Honestly I feel 5% is just too low- it takes too many jumps for the enemy to lose a noticable portion of their fleet to make a consistent difference. Honestly I'd rather just see the convert chance bumped up to 7.5-8%- whether you keep convetered ships or not, removing 7.5-8% of the frigates in the enemy fleet makes a fairly noticable difference even if the enemy only needs to pull back from an attack only once.
