Settings in calibre are in two places: the library database and the configuration folder. The database is in the library. The configuration folder is normally in appdata but can be moved using an environment variable (I do this).
Check where calibre thinks your configuration folder is located by starting calibre, going to Preferences / Miscellaneous and clicking on Open calibre configuration folder. Make sure that the folder that opens is where you expect it to be. If it is not then
change the environment variable CALIBRE_CONFIG_DIRECTORY to tell calibre where it is.
If it is where you think it should be but your plugins are not in plugins subfolder then you should copy the previous configuration folder into the current one.
Note that the timestamp of some files such as gui.json will change every time you run calibre. If this is not happening in what you believe to be calibre's folder then you and calibre disagree about its location.