Problems when copying/pasting from one sequence to another

So, I've been working on a large project for several months now. I've been editing each segment in a different sequence with the intention of bringing them together one at a time and adjusting the transitions between them. However, when I copy everything from one sequence and paste it into another, I'm encountering several problems. The one that concerns me the most is the audio differences. I'm using quite a few J-cuts in this project, and I've spent a lot of time tinkering with them to make everything sound natural, but a segment from a copied sequence appears to lose all of these tweaks. The worst part is, there does not appear to be any actual changes in the editor, but I can clearly hear the difference when I play it back in each sequence. I would basically have to do all of the work again to recreate it. The other problem I've run in to is a drop in the frame rate on some clips, usually clips that are layered on top of other ones. I've exported a test video, and both of these problems remained in the exported file. This problem doesn't occur if I paste a segment into a new, empty sequence, only when adding it to an existing one.

I am open to any suggestions on how to fix these problems, or alternatives to how to edit this project (I don't know how conventional what I'm doing is). I know that I could simply export each sequence and string them all together, and that's what I will do if I cannot figure this out, but I lose a lot of freedom for the rest of the editing process by doing that. Thanks in advance for any responses.