I see this subject has appeared before and I have something very similar, but quite repeatable. I first tried RPD some years ago but it didn’t fit my workflow and am now trying again with v0.9.17 so the sqlite databases are still small.
The symptom is that after a successful download, adding even a single extra photo to the SDCard, all photos on the card are reselected for downloading again. Remove that photo and all is fine again after a rescan with nothing selected for download. Add it back and the problem returns.
Examining the downloaded_files.sqlite database it contains the expected data with previous downloads recorded correctly.
However examining the thumbnail_cache.sqlite database will now show a duplicate row for every file on the card but with the new row having a different mtime field value. All other fields are the same. The difference in time is exactly one hour and I suspect may be due to an error in summer time evaluation on the second scan.
A comparison of mtime between two such duplicate rows is shown below:
date -d @1568892080
Thu 19 Sep 12:21:20 BST 2019
date -d @1568895680
Thu 19 Sep 13:21:20 BST 2019
I can furnish logs and the databases if it may help.