As I said above, they probably aren't actually missing, but the game is detecting an old version of the mods attached to character cards that is no longer installed. Even if you have a newer version of the same mod, it only counts what was last applied to a character, so the character card now has a version applied that is no longer installed because a newer version was put in its place.
All you have to do, assuming the above is the problem as usual, is take accessories and other modded parts off of characters and then put them back on. This will swap the old version for the new version.