Nope, the map files are in their chosen slots, and cannot change. If MAP01 gets replaced, then the last mod replacing MAP01 is gonna be what remains. Same for all the other slots. You could rename all the map files and merge all the level headers together and change which map slots the entries point to, and merge them all into one mod, but such modifications to other works is frowned upon and not allowed to be shared, so if you wanted to do that for your own private use, you'll have to figure out how to do that on your own. In addition, if any maps have custom objects, any mod using their own custom objects may use the same object numbers for their own objects, meaning you would have to change those numbers, then extract the maps from the PK3, load the WADs from the PK3 into Zone Builder, change the numbers in there too, then test it all th make sure it all plays nice and that none of the SOCs and Lua scripts conflict with eachother from mixing mods together.
TL;DR - Nope, and it ain't worth trying to fix it yourself.