There is no correct answer to your original question. Both are stable and are used by people for various reasons. Occasionally settings from a previously installed version have caused problems That is not the rule but rather the exception. I have used both Lubuntu and Xubuntu and have settled on Lubuntu. It is fast even on an older system with less RAM. You have to consider what you want to do with your computer.
As to deleting the .folders, I don't think that is a good idea. Which applications are crashing and under what conditions? If there are just one or two, it is better to deal with them individually rather than trying to remove a wart with a machette.