Currently, when you hit the option to Sync Grades, the pop-up list is filled with all items that you want to sync. You can then check or uncheck items from that list. THAT list is built based on what assignments have sync turned on. If you have older assignments, maybe from a prior quarter or semester, I suggest turning of the sync for those assignments. You can do that on the Assignments page by just clicking on the sync symbol on the far right for each assignment you want to turn off. So go from green to black in color. This will reduce the list in that pop-up. Depending on which SIS you are using, this could also reduce some errors that can potentially hinder the sync process.
Beyond that, there is not a way to filter the list that I have seen yet. Another option to consider is going to Sync Grades on the left course navigation list and turn on Nightlight Sync. This auto-sync everything over night (the exact time varies). The only time I use the Sync to SIS option on the Grades page is when I am updating some last minute submissions right before a progress report it produced, of if a bunch of students have been trying to get caught up before a grade check by their coach.