Expressions do not get updated if you pre-compose a layer that has an expression which references another layer. First I hope you saved your project before you made these big changes. I never ever work on a project that has more than one or two layers without increment and save turned on. If you don't have a copy and can't get back by pressing undo then you will have to look at every layer that's broken and move the reference layers to the right pre-comp. There is no way any of us can help you without a flowchart and specific error messages from each broken expression.
The problem was that It saved right after the precomp was made on its own. I've been going through it and looking at everything (crying deep inside the whole time). There are 10 Compositions each with 30-40 more compositions inside with some comps going 5-6 deep. There is a total of around 800 layers or so.. none of that really matter aside from the controllers (These are the ones that are really messing everything up). Some stuff was changed a lot and I've no idea how (colors for effects, keyframes, sizes, and shapes).
It is looking like I may just need to take the rest of the week off and go on vacation... ha.. ha..
Anyway, I've saved a version of the current file I am working on separate from the save that happened during the precomp destruction. I'd have a hard time giving an accurate flowchart and there were around 30 error messages. Is there a way I can look up those messages?