Subversion integration problem

Recently I upgraded from SCC provider to subversion plugin in source control
Then did bit of tidy up such as deleting old unwanted projects , restructuring directory structure.
Did manage to arrange everything and looks perfect in TC, Win Explore and SVN repository.
Everything work fine and did updated some changes as well.
But while doing a commit there was a message saying could not committed and TC lost connection with subversion.
(Looks like no subversion at all -without icons)
try to commit in win explore said SVN has to clean up. After clean-up process some files were missing.
Those were files I replace while tiding -up at beginning
Luckily in SVN repository they were there
Anybody has any idea?