Downstream bug: https://bugzilla.redhat.com/show_bug.cgi?id=738084 Basically a display changed names from VGA1 to VGA2 and settings had to be resetup. It should be possible to store display settings based on their EDID data instead of xrandr name.
What do you suggest to do when people use two identical outputs (same brand, same model, etc.)?
I guess you have to choose something. ;) Save the config as the pair of them? (danger of them swapping between each other) Just save one of them (no worse than now?)
This bug has been fixed here and released as part of 4.13.5: https://git.xfce.org/xfce/xfce4-settings/commit/?id=b692780cdce46447cebb4af410da5b0b355e6eb5