Rasa X local fails to sync up with the local repo

I did a hard reset in the local repo, but it changed the local repo whenever the local rasa x restarted. I expect the rasa x to read from the local repo, but it goes the opposite way. Rasa x updates the local repo.

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And when I split an NLU file into two, Rasa X keeps the old big file AND adds the new file.

What I do is disconnect Rasa X from the repo and then reconnect. But a lot of times I click on “Disconnect” and it stays connected…