How to clear source code cache on master keeping it working?

Hi.

I got TeamCity master have corrupted source code cache inside. One of projects is using some branch which is coming to agent via Server-side checkout. So after something happend (I don't know really, may be TFS was inaccessible) this project has failed almost all its configs because the builder couldn't find some necessary files to use. I've checked all agents where configs of that project have failed - they all missed the same some necessary files. Rebuilding with clean checkout didn't help. After I changed vcs settings to Agent-side checkout I got config built
successfully.

Question: Is there any way to keep TeamCity master working and clear source code cache? If yes, how to make it as smooth as possible?

Bulat

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