When 2 databases are open and the user views database A while in database B changes are committed by another user/instance the review changes window appears. If the user clicks on it and accepts changes while viewing database A, the groups in database A will be overwritten by the changed database B.
Thank you for reporting this! I can confirm this bug, and will make sure it is fixed in the next version.
Related: https://sourceforge.net/p/jabref/bugs/999/