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First of all, check that your VCS settings in IDEA correspond to the VCS settings in TeamCity.
If they do not, change them and it should fix the problem.

Secondly, check that the build configurations you expect to be suitable with your IDEA project has either server-side VCS checkout mode or agent-side VCS checkout mode and NOT manual VCS checkout mode (it is not possible to apply a personal patch for a build with manual checkout mode because TeamCity must apply that patch after the VCS checkout is done, but it does not know or manage the time when it is performed).

If the settings are the same and you do not use the manual checkout mode but the problem is there, do the following:

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