So here's a 'sort of' answer.
With the attribute manager you could overwrite layers from one file to another. The process would go something like this:
open the file with the bad layers. (file A)
open the attribute manager.
on the right open a file with good layers. (file B)
Overwrite layers from the good file (B) onto the bad file (A), the layer names will be replaced, but the numbers will stay the same. (overwrite looks at numbers, not names).
If the numbers correspond, and there are no holes, then the overwrite should be done. The problems occur when there are holes in the sequence. You have layers 1-45, 48-90, 93, & 95 in file (B) and layers 1-100 in file (A). In that case you'll still have junk layers, but less of them.
Anyways... once you've done this (ideally with no holes in the sequence), you'll have good layers in file (A). This means you can copy and paste things out of it, without bringing over crap layers. However what will almost definitely happen is everything is on the wrong layer. Your walls might be on the plumbing layer, your roofs might be on the text layer, etc. At least they'll be layers that should exist in the new file, so it's just a matter of changing their layers in file (B). Which shouldn't be too bad. Maybe.
Clear as mud?