Taxonomy terms lost on conversion

I started a site with 'normal' content types story, page and forum. Now it has outgrown its organisation and I'm in the progress of converting nodes to customised content types including cck fields.

When I convert a node which had several taxonomy terms assigned to it (via autocomplete active tags free tagging) the terms loose connection to the node in its new type.

Before the conversion I made sure that the new content types were included in the vocabulary used in the old content types.
This is a rather bad thing, as these terms are still a major key to the organisation of the nodes on the site.