[melba12]

I hope you have by now resolved, but reading this 3d I've devised my own way and did it, so I report here, cause I had the same issue with Calibre 4.2.0 (downgraded from 5)
1 create an empty new library by copying the structure to and putting it in a different file from the original one
2 select all your books and copy them all into the new library
3 switch to the new empty library and, most important, close Calibre
4 reopen Calibre and you will find that you can delete all you need
5 now you can delete the old library and also all the files and the db contained in the old position

For me it at worked spendidly!