Great Scott! I think i got it.
So after disappointment with the fact that on 11.5 the recofigure-all switch seems to be deprecated, I realized that the FTP user accounts were still showing up in the Control Panel view of the domains. I then reset the password for the FTP accounts from the...
I have the same exact issue as TaxiCK.
I ran the --remove-all switch and it did exactly what it was supposed to, remove all FTPs.
However, I went to run the --reconfigure-all switch and got this: Command not supported.
WTF! Now i have to rebuild all those FTPs including the FTP setup...