Unfortunately, I don't think you can. The association between the Flickr Publish service in LR3 and the Flickr photo itself is maintained in Lightroom's Catalog. It doesn't seem to be exposed in the interface. You would need to hack in the LR3's SQLite database to change this bit of info, or create a plugin.

But wait. One way to associate your Flickr photos back to your pictures in LR is to use Jeffrey Friedl's “Export to Flickr” Lightroom Plugin. I don't use that plugin anymore since I switched to LR3, but it has a little known feature that could help you. Select the photos you want to associate in LR, then in the "File -> Plugin Extras -> Flickr Extras" submenu select "Associate Images". The plugin will try to find the corresponding photos on your Flickr by matching capture time. The association (i.e. the Flickr photo URL) will be displayed in the plugin metadata in the right panel.

From there, I think you can crop your photos in LR and use the plugin to update them on Flickr. You won't be able to use LR's Flickr Publish service for these though, because it is unaware of the plugin's metadata that stores the association. Give it a shot?