Checking in to say I’m also experiencing this issue (deleting empty folders) with the Remotely Save plugin! ;w;
I have S3 set up, Obsidian & the plugin are all up-to-date (I just fresh installed them earlier this week), was experiencing this both on my computer (windows 10 & linux) and Android phone.
For now I’ve had to create placeholder notes in the folders so they don’t get deleted :')
Hi!! Was playing around with Remotely Save settings again this morning and figured out how to get it to stop deleting the empty folders!
Change “Generate Folder Object Or Not” to “Generate” – the setting is at the bottom of the first section where you set up the S3 settings just before Check Connectivity. I’ve had no issues with it syncing my empty folders now across my devices as I try getting my stuff organized👌🏻