Upgrade to Retropie 4 deletes ES custom folders

[UDb23]

Just upgraded, thru binaries, from Retropie 3.8.1 to 4.0.2.
Process went well apart from Emulation Station; I had custom folders for themes I added to Carbon: the upgrade deleted all these folders. I suppose the upgrade procedure deletes the whole Carbon folder and recreates only the standard systems/themes related subfolders.

Customized Es_systems.cfg can be protected by placing it in /home/pi/.emulationstation; unfortunately that doesn't help if related custom theme subfolders are deleted during the upgrade.
Apart from backing up and reinstall the custom folders manually is there any way to protect these folders ?
It could be nice to have an option for ES upgrades that asks if "additional" directories inside "Carbon" folder should be kept or not.

[herb_fargus]

@UDb23 the same applies to themes. Any custom theme changes you make put in /home/pi/. emulationstation/themes and they won't be overwritten on updates.

[UDb23]

@herb_fargus that was a fast answer ! Thanks; wasn't aware of that. Will keep it in mind for next upgrade :-)

[herb_fargus]

@UDb23 yeah it's a little hidden in the wiki, perhaps I'll make it a little more verbose:

For reference: https://github.com/retropie/retropie-setup/wiki/EmulationStation#my-es_sytemscfg-is-being-overwritten-on-updates