Okay so here is this issue. so the entire animation, within one pre-composition. On the photoshop file, I built the animation, the designer added 3 global effects to it. So I did the same thing here. you can see in the first screenshot
So here the preview I'm seeing in aftereffects is 100 percent correct. so I bounced it in Media Encoder
The preview here is also 1000 percent what it supposed to look like.
when I check out the final file. I get this below, with none of the added effects to the pre-comp.
Really not sure what's doing this, here are some things I tried.
I took the video and added the same effects in adobe premiere and had the same thing happen where the preview looks right. the media encoder looked right but the output file didn't have those layer adjustments.
I bounced in apple pro-res, h265, blue-ray DVD, all had the same issue, just ignored the effects
I created a new AE project file and dragged the video and recreated the effects to no avail.
I put everything (the first image in a new pre-comp) and then tried to render it within ae and the encoder. No luck.
it would show the correct preview but when outputted the layer changes would not be there.
I couldn't find anything related to this and it's been driving me up the wall.
I'm not clear what you are trying to say here. Your AE screenshots clearly don't actually show Comp 5 according to the breadcrumb bar at the top, but rather some nested comp used in the parent comp. So we therefore have to assume that there are other layers involved. Chances are you used some layer switches like solo layer and then overrode these options in your render settings when simply setting it to best quality, which toggles such switches. Other than that there could be of course something weird going on here due to your 3D comp with the collapsed transformations or your imported PS layers' layer style having an effect on rendering order as well as AME having a bad day and just ignoring some settings or not rendering it correctly due to hardware acceleration failures, but without more info we honestly can't tell. Start by checking what I hinted at - look for conflicting layer switches in all the comps, verify your PS layers, check the render quality settings.