I just thought of another possibility - that you are maybe seeing on the Source (which is correct) files which have very similar but slightly different names. This can happen with software that generates temp copies of files with 'versioned' temp names (often related to / based on the real filenames), then eventually deletes them during 'housekeeping' (perhaps as that software is closed).
If they were copied by SB before that deletion (thus, now present on the Destination), but are not on Source now (under the previous name) but they are there now (under a similar but slightly different name) confusion can easily arise. SB may very well be proposing to copy the current version (new slightly-different name) and delete the old one from the backup. Check the file-names on each side very carefully...they may look similar at a glance, but may not match exactly.
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