I have been working on upgrading my flashnode module for Drupal 6 and I see that the {files} table is changing and nid is being dropped.
Flashnode (for D-5) currently uses nid to link entries in the {flashnode} table to entries in the {files} table. Earlier versions of flashnode used to store both nid and fid, but because the {files} table had both of these I stopped storing fid as this could be derived from the nid alone. Maybe that was wrong at the time, but anyhow, that's how it works.
The problem is that with D-6 the nid gets dropped and replaced by uid, so existing content will have no way of establishing the connection between flashnodes and files, post upgrade.
One option is to write a pre-upgrade routine for flashnode, to be run on existing D-5 sites, that will amend the {flashnode} table to add in the new data. However, I am fairly sure some people might dive in, upgrade, and then realise their content is broken.
Just a thought, and it may be late in the day, but would it be possible to make a table available that holds old fid/nid pairs that modules could refer to after an upgrade? That way a user can follow a simple upgrade path?