When reinstalling my distro, I accidentally deleted my user account by forgetting to select for preserving it (a mistake I rarely but occasionally make), and restored it from backup. But since the backup procedure in Luckybackup did not have "delete files on destination" selected, the backup gave me a copy of my user account that was more-or-less up to date (a few hours old) but full of files I had long since deleted. I had to take some time to clean up the mess, and probably haven't found all unwanted files yet.

Therefore, I am considering selecting "delete files on destination" (which I assume means delete files the source lacks) but...couldn't it backfire? I might delete files from my user account by accident (or they might become corrupted or something) and then have no backups of them.

Your choice. Personally, using another backup program, I get it to delete files from the backup that have been deleted on the source filesystem (essentially the backup ends up being a mirror of the source filesystem).

However I also take weekly images of my partitions and keep a rolling couple of months of these. This means that I can get my hands on deleted files for that sort of time period, although the principal reason for the images is actually for complete system rollback if it is needed.

This backup mechanism hasn't failed me yet. If I haven't noticed a file missing after a couple of months then I don't need it anyway.

If you're not going to take any alternative occasional images/backups, and potentially losing a deleted file worries you, then you should perhaps find a backup program or mechanism that makes incremental backups and allows you to restore various versions of the same file that were backed up at different times, as well as restore all files existing at the time of a specific backup.