Unfortunately, you will have to prestige to get back to rocket fuel meaning you will have no opportunity to make soul egg progress. However, what I do is unlock the advanced rockets, and then, launch an extended rocket while Prestiging.

Then again, you don't have to be launching rockets, but I can understand your situation.

You can still make soul egg progress while you are waiting for your rockets to return from their missions. After you launch a set of missions, upgrade to the highest egg you can, and work on soul eggs from there until you have to prestige to fuel the next round of rockets.

Waiting on Fusion for 3 hours straight to get 3 short Quintillion Chickens fueled is SOOOO FUNNN (thanks auxbrain (that means screw you auxbrain btw))