Originally Posted By: tanstaafl.
If a source file changes, that file is deleted from the backup and replaced with a new copy of the changed file.

The rest of your system seems pretty complicated but if it works for you then I won't argue. But this worries me a little, and leaves you completely susceptible to ransomware. I've had several clients get infected with ransomware, which changed the files by encrypting them, which then triggered a backup of each file. By they time they catch on to this, usually most of their files are already infected AND backed up. But it's no matter because most backup services offer versioning so you can merely restore all the files from right before the infection occurred (after cleaning it off, of course).
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Matt