Inconsistence between active and inactive workspace

I experience a strange issue connected with DC deletion. I followed the steps provided by 864515 note, and all went fine until I tried to delete .dcref files of target DCs. Activation of this activity failed and things became so that DC were deleted from inactive workspace buut they are stil present in active.

Then I tried to delete that DC in Web DTR with the help of web activity in that way

but the process again failed with the error "Error: Precondition integrate-of-version-sets-not-allowed check failed."

To put it more clearly, the current situation is:

1. DC files/folders are successfully deleted in inactive workspace, as well as their .dcref files in TopLevelDCs folder.
2. But all these files (DCs + .dcrefs) are presented in active workspace still.

What is the proper way to fix this problem?