Changing VCS Username causes error when retrieving from TFS

We have a VCS root set up connecting into TFS and working fine. I now want to change the user that TeamCity is using to connect however when I do this and try to run a build I get the error:

Failed to perform checkout on agent: Failed to perform TFS clean checkout. [2016-11-23 17:10:11,382] ERROR - JetBrains.TeamCity.Tfs.Program - TF14061: The workspace TeamCity-checkout-13f15709db0e4e88926d6b6c7270bba0;SVCxxxxxxx does not exist

We've got more than 20 VCS roots set up so I don't want to have to re-create each one with the new details if there is a way. I've tried clearing the cache as detailed in the link: https://confluence.jetbrains.com/display/TCD10/Clean+Checkout but that hasn't worked.

I guess that a possibility is to turn off the clean checkout for the first run it does as a new user but again this seems to be something unnecessary.

Does anyone know a way to do this smoothly?