As for the latest Patch to the Game. Will this change anything regarding your tool?
As long as NMM doesn't change they way it internally stores mod data, everything should work fine.
NMM 15.x now requires validation of the game installation path (called skyrim directory in the config), so that pretty much makes the tool unuseable until a workaround is found.
You may be able to just install NMM 14.2 (in addition to the current version) to a different directory and use it only for conversion purposes, as long as different versions don't share the same config files it should work.