Periodic Manual Large File Sync using External Drive Possible?

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I'm looking for a working solution for a current use case that I have. I run Risilio Sync between two remote locations keeping six various directories in sync. This works very well for the normal amount of files that are added/modified on a regular basis. Every few months there will be a large amount of new files or modifications to files (~1TB) that will originate in one directory or another. Due to the limitations of the WAN speed, this sync could take weeks or months, long enough that the sync wouldn't complete before having another large file dump to sync. Is it possible to copy the directory from the source machine to an external drive and use rsync (linux rsync not Risilio Sync) on the destination directory to add/replace the folders and files in the destination directory, and then resume Risilio Sync operations to keep the directories in sync after that?

I will say that I've attempted this procedure a couple of times now, but I fear that I've been copying files that perhaps I shouldn't be to the external drive, like the .sync directory. Perhaps there is an order of operations that would allow this to work successfully. I'm just curious if anyone has tried something like this with any success. Pulling the storage server from Site A to visit Site B for a couple of days for a local sync is hard on the back as it's quite heavy.

Thanks in advance for any helpful information.

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