If you renamed application folder that should not break the application items because it uses relative pathes (only items that links to files under the [Mouse Extender] folder could be broken).
For example MouseExtender app folder is:
"d:\ME\mouseextender.exe" (and other app files here)
Imaging you have added item that links to "d:\Games\SC2\sc2.exe". Program will store relative path:
item path = "..\Games\SC2\sc2.exe"
From now if you rename application folder to "MouseExtender" (for example):
item path will still be valid and application could be laucnhed and proper icon displayed at ME.
Please, let me know if I understand you case in proper way