Hello,
Is your online backup automatic or do you manually schedule it? The online backup wouldn't work only when Method is doing a changes only sync and you can see when it is performing the sync by opening the engine and looking at the status. If you are manually doing the backup then you can push it between changes only syncs.
If you are doing automatic backups then I can brainstorm with the Development Team to see if it is possible to maybe pause the engine for a specified period of time so the backup can run and then resume afterwards - this is just an idea that I can bring up. I'll wait to hear back from you.