You aren't the 1st one to get bitten by that one. That used to bite me every once in awhile for no particular reason...and would stump me for literally hours each time.
To cure it, awhile back I started a completely separate partition just for MPLAB, PBP, MCS, PICKIT2, all my programming stuff and keep it all in the root directory.
Even if I do have to type something out at the command line, the line ends up being relatively short. Not to mention, I can 'dynamically' adjust the partition size with Partition Magic since the partition is so small. And I backup the whole thing at PC startup with a simple ZIP batch file straight to a thumbdrive. Practically bullet proof...and transportable...
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