When the RadControlsSP.wsp
is retracted from the farm all the default files in the /Program Files/Common Files/Microsoft Shared/web server extensions/wpresources/RadEditorSharePoint/x.x.x.0__1f131a624888eeed/Resources/ folder are deleted. When the solution is deployed all the default files are added or overwritten.
Unfortunately currently the only solution of your problem is to backup your custom files (or the entire Resources folder), so you can restore them easy on an upgrade. Keep in mind that in the upcoming new versions the default configuration files might be different. So the best approach on upgrade is to merge the new default files with the customizations you make.
I am sure that this information was provided in our online help, however currently I could not find it. I contacted our documentation team and this will be fixed ASAP.
the Telerik team