Lou,
I use an S270 with the MRC1. I think the IDX files just keep track of the previously recorded files. I have 'file copied' just the .M2T files to the NLE and not seen any issues.
Using Vegas Pro to offload the clips, the names are binary and very hard to identify and the IDX files are also transferred, though they don't seem to be useful.
Perhaps if the .M2T files was larger than allowed by the FAT file system of the CF cards, the IDX files are used for reconstruction by the SONY Recording Utility.
HTH
Cheers for now,
Tom Pauncz
(30WEST MEDiA GROUP)