It just dawned on me you said you deleted the internal Firefox files from BOTH locations. A properly functioning Windows should resolve either reference to one and only one directory. Possible filesystem corruption? Windows is very tolerant and tries to work around small issues. A minor filesystem corruption may be difficult to positively diagnose. If your main drive and home are not encrypted, you could try booting from a USB based Linux distro and see what your directories look like. Unless you get an obvious filesystem error, you really haven't learned much.
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