You can rename the folders to one of the Unity's 'Special Folder Names' and they will be ignored: If you're on Windows, setting the folders to 'Hidden' would probably be the easiest as it likely won't be picked up as a 'change' by version control.

During the import process, Unity completely ignores the following files and folders in the Assets folder (or a sub-folder within it):

 

• Hidden folders.
• Files and folders which start with ‘.’.
• Files and folders which end with ‘~’.
• Files and folders named cvs.
• Files with the extension .tmp.

https://docs.unity3d.com/Manual/SpecialFolders.html

You can rename the folders to one of the Unity's 'Special Folder Names' and they will be ignored: If you're on Windows, setting the folders to 'Hidden' would probably be the easiest as it likely won't be picked up as a 'change' by version control.

During the import process, Unity completely ignores the following files and folders in the Assets folder (or a sub-folder within it):

• Hidden folders.
• Files and folders which start with ‘.’.
• Files and folders which end with ‘~’.
• Files and folders named cvs.
• Files with the extension .tmp.

https://docs.unity3d.com/Manual/SpecialFolders.html