Yup! I’d also directly-connect my phone to my computer and do a backup via the Finder/File Explorer into a totally different backup directory before I delete everything, though, just to be safe.
(There may be a reason why I needed to write a good de-duper for PhotoStructure…)
I think pixels just do this. I don’t know why. PhotoStructure is happy walking into any directory, though, and if it’s empty, no big deal.
If the sync runs later, and there are suddenly files in that folder: again, no big deal, they’re be imported.
If you have a Pixel, you’ll have full-quality backups if you pull down a Google Takeout. If you’re on a Mac or Linux box, you can then use ratarmount to “mount” all the tarballs into a single, merged directory (without taking all the time and disk space to uncompress everything!), and let PhotoStructure sync from there too.
I discussed ratarmount in this post, but I’ll make a proper instructions page soon that outlines exactly how to do this.