If i switch from main file to the follower mod compatibility file will it reset my progress with my 3DNPC companions? Also when i try to dismiss zora she still follows me will this effect my un-installation of 3DNPC?

Generally if the different version has a different file name (i.e. the ESP is named differently), then the progress won't carry over and it'll be treated as a new mod.

and what about zora who wont stop following me after i dismiss her?