If a file is deleted inside the project workspace, it will not be checked out again by the Integrity-Plugin. However this can be done with Jenkins by using "Wipe Out Workspace".

As far as I have digged into the code, the layout of the last checkout is persisted in a file. This information is then used to compare with the current MKS data in order to decide which files to update.

I thought deleting "viewproject.dat" would be a workaround for this problem, but it didn't help