It is also worth noting that if you go to a record in calibre and select the 'Edit Metadata' option - in the top right hand corner is a list of available formats for that record. That box allows you to add, remove (and import metadata from) specific formats.

It is possible to remove all the formats and leave just the record and metadata but with no actual file attached - so delete the Doc file but leave all the information there. Equally, you can just add new formats into the record and leave the Doc file for completeness/archiving.

So, for example, you could just add the RTF and/or HTML versions to the record. Then when you go to convert to the format you want, when you go to the 'convert' page you select which of the formats you want to convert from the 'input format' dropdown in the top-left hand corner and convert away.