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I just updated to 2018.4 but using the input tool I seem to be missing network drives, there's also some showing that I do not have mapped. Even if I use the recent list to browse it claims that the drive doesn't exists when Explorer clearly shows it as a mapped drive.
I'm missing my O, R, W and X and Alteryx has a mapped S,U and V drive that don't actually exist. Seems like some old cached network list from long ago.
I had a very similar issue. It seems to be a symptom of Alteryx running in 'elevated' mode which happens after launching from the installer as the installer is run elevated under administrator privileges. When closing and reopening Alteryx, you open it under its normal non-elevated running mode.
You can always check the status of elevation by going to Help > About.