To synchronize, I first selected the X folder, then changed my mind and selected the Y folder. Yandex.Disk synchronizes the contents of the local folder on its own, i.e. without waiting for a user request.
Because of this, both folders are now almost identical. Almost - because the synchronization can be stopped. Although, I suppose, this scenario of synchronization of local folders using Yandex.Disk is not 100% obvious.
To return to its original state, you will have to roll back to the restore point.
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Conclusion: before playing with Yandex.Disk, set up backup and recovery of data and make sure that you can recover data that will be accidentally corrupted by this program.
Wish: make a widget for Windows (Vista / 7).