Please note that I have updated the BIDS conversion of MEG recordings and the empty room noise recordings will no longer be moved to the sub-emptyroom folder but will stay with the subject data. If you want it the “old” way, then you can explicitly enter emptyroom as the subject ID during MEG acquisition for your noise recordings.
The reasons why I switched have to do with simplicity and the ability to share anonymized data with shifted dates. While not the recommended organization in the BIDS specification, this new way is still BIDS compliant. This was discussed on the BIDS google group.