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[SOLVED]
It turned out in the end that the problem had arisen because when i re-assembled my PC, it had exchanged the Drive letters of the two external drives. So, Drive E had been labelled Drive F, and vice versa.
This had confused Minion, and as it turned out a lot of other programmes, that suddenly couldn't find the folders they were looking for.
Once I realised the cause it became relatively simple to switch the Drive letters back again and magically solve all the problems at once. I now have a dummy folder on each drive called 'Drive E' or 'Drive F', so if it ever happens again I know which is supposed to be which.
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