Hmmm... To delete all the files just delete the fldigi.files directory. Fldigi does not use any files outside that directory unless you have specifically told it to do so and that would be configured by settings within the fldigi.files directory.
You can test for that by going to c:\Users\<loginname>\fldigi.files and rename the flidigi.prefs file then try to start fldigi. If that works then you're good to go. If not then rename the fldigi_def.xml file in the same directory. That will cause you to need to setup fldigi from scratch. Just do a basic minimal setup then close fldigi and restart it. If it's ok then finish reconfiguring fldigi. You'll still have macros, logs, etc from the old config. It that doesn't solve the issue then go back and delete the newly created fldigi_def.xml file and rename the old one back to fldigi_def.xml to restore the old config.