I had some great help from fellow EE experts. The probem is, that when the command is run, it not old deletes all the files but also all the data from the logged in profile.
This is the command I ran:
for /f "tokens=* usebackq" %a in ("C:\Users\archiver\Desktop\tagRemover\file.txt") do del /q /s "%~a"
This is a sample of the may lines I have in the text file for deletion(note: They all have quotations around the file path in my file.txt):