Source Control Bug

Hello everyone! Hope you are having a good day with no bugs.
Our Team is working on a game project using the GutHub (LFS) for the source control. Our project mostly done with the C++ Scripting and then we are creating BP driven from those codes. The Problem is when we are pushing and pulling the changes the Blueprint files are giving crash pr even getting deleted. So we have to rebuild Blueprint with all its settings. It is happening when we are merging 2 codes. But one time it even deleted the Game Mode which was not touched at all. C++ files are fine so far.
Could you tell me if anyone faced the same issue ?
We did not even figure it out whether it’s happening due to the Unreal Engine or GitHub