Adobe Media Encoder grabs the wrong After Effects source file

You're welcome. And don't worry about the project, 17.0.6 and 17.0.5 all use the same project format of 17.x. If something goes wrong (which won't happen), then you can upgrade to 17.0.6 again. In fact, I've been working on the new Public Beta of AE since it was released and I can go back and forth from 17.1.x to 17.0.6 with zero problem.

The beta is also another option as I believe the fix for this issue is already implemented there. I haven't had any problems sending my comps over from AE (Beta) to AME (Beta).

I recently learned that there is a known issue with sending AE comps to AME via Dynamic Link in AE 17.0.6. You can try to roll back to 17.0.5 (make sure to go back a version of AME too) by going into the CC app, clicking the three dots next to the "Open" button, then clicking "Other Versions."

As for how to export a ProRes file out of AE. Yes, you can do the MXF version, which will likely create a couple extra data files you don't need, or you can click on your Output Module in the Render Queue, change the Format to "QuickTime", then click the "Format Options" button and choose "ProRes 422." See the attached screenshot for the Output Module Settings.

I wonder if you have some temp file that's causing an issue here. I would save a new version of your project and also delete any folders next to your project file THAT YOU DID NOT CREATE, but contain "AME." Then try again.

Alternatively, you can always go the traditional route and export a master file out of After Effects using a codec such as ProRes 422, then convert that to H.264, or whatever your final delivery format is, inside of AME. Depending on the complexity of your project this can actually be faster than trying to export directly to H.264.