In the most recent patch update, a new setting was added to the Google Classroom Integration. Overwriting with Blanks is now an option in the gear icon from the Google G. This setting determines if blanks in Classroom can overwrite scores in Synergy. One example would be if you manually added a score in Synergy that was not in Classroom. If this setting is set to Allow, the score would be blanked out, since Classroom is blank for that assignment.
Keep an eye out for communication regarding updated resources for the Classroom Integration, and how to access them. We hope to have these available in the coming weeks.