Is there any way to prevent enemy capships from self destruct upon arrival at nav point.
I had this bug several times, especially in G'Wriss system mission2 (all versions)
I recall an issue where the Midway would count as destroyed upon launch, though I don't remember the exact circumstances. (But if these are Nephilim ships, don't you want to, sort of, accept this turn of fate as a boon granted by the imps in your CPU? ) Try starting simulator mission 7 and see if it helps.