Ok, to clarify: on any editing you've done to the fake players in either of the two fake leagues, the only thing that you will likely 'lose' is that their nationality will get set back to default. You'll have to go in and fix those.
You won't lose any editing to the teams -- like team names, kit templates, colors, PNGs, etc. They should be ok.
The rosters for the clubs in the two fake leagues will get scrambled. The fake players will go back to their default teams. You'll have to use the transfer option to shift them around if they're out of place.
When editing the MLS file, I tried to do it so that there would be a minimum of shifting around of players, but many players will still be out of place.
Another thing I didn't mention before: team settings, formations, kick takers, etc. for the fake clubs are likely to be re-set, as well. Have to do that over, too.
In terms of whether you've moved teams around via the 'edit league structure' option, that shouldn't be too much of an issue. You just need to get the players on the right teams; then you can move the teams however you'd like.
There's a list of players who are likely to have disappeared with the DLC here, in case you wanted to base-copy any before you d/l the DLC:
http://www.pesgaming.com/showthread.php?t=82645