I had a similar issue.
Please check this thread Syncthing-Fork using the wrong path it provides explanations and workarounds.
In my case, I was able to keep my folders as /storage/emulated/0/foobar outside of the new syncthing home folder (~ now means /storage/emulated/0/syncthing). The trick was to update the path directly in the advanced settings. Backup your data before doing this.