How to switch to or merge the partial branch after migration from CVS?

I migrated code from CVS to Gitlab and I encoutered a problem about the branch.
Some branches in CVS are just contain some specific folders,not all the folders. When I switch to these partial branches in Eclipse, and the pakege explorer just disappered because the branch is not contain all the folers and the .project file.
When I sueccessfully switched to these partial branches in Tortoies Git, and changed the code.I created a merge request to merge it to the master,and I got a 500 error on the Gitlab.
So how can I fix the problem?
Am I must go back to the CVS and modify these partial branches to contain all the folders?

   I would greatly appreciate it if you kindly give me some help with this.