Hi Dan,
I never actually tried this as the next update to CCS (5.5?) had sufficient updates to the EGit plugin to fix the issues I was seeing. What CCS version are you using? CCS 6 uses 3.0.3. I believe this may be advanced from previous CCS versions but the Eclipse website says the latest EGit version is 3.4.1, though attempting to run the update within CCS tells me there are no updates. I guess this means this is the latest supported version for use with the version of eclipse used by CCS 6.
It seems to be working OK for me so far (only had v6 installed for a week or so). I havet come across any other bugs in the older versions of EGit I had been using ill recently either. Was there a particular issue you were trying to overcome by updating?
Anyway, to solve the issue you are seeing now my first recourse (though I'm no expert on CCS or eclipse) would be to just uninstall CCS and reinstall... If eclipse wont uninstall you can just delete the install folder (usually C:/ti/ccsvN (where N is the version number) and then run the install for the new install over the top.
Hope that helps some :)