After Effects composition will no longer populate in Media Encoder.

Hi guys.
I'm pulling my hair out with this recurring issue with Encoder.
Ive been working on a 24 minute or so video and i have made a habit of stopping every couple of minutes to check if Media Encoder will pick up the composition. 2 hours in and its still appearing, but 30 minutes later it no longer appears. No matter how far i back track, I cant make it appear again. This is the 3rd time its happened and with so many hours invested into this, I really don't want to do all that work again.
Do any of you know what causes this issue or better yet, a way to fix it?
Ive tried rendering through After effects manually but the video is always too big and I it never has audio and has choppy slowmo pictures.
In summary, i don't want to do 12 hours of work all over again. Please help.

We can't know anything. You have not provided any system information, no exact version info, no comp settings, no details about footage and effects used and a gigazillion other things like cache settings, AME settings and so on. I don't even know where to stop because so much info is missing....
Mylenium

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