Did you have an add-on in XF1 that provided BB code media sites? If so, that is likely the cause and in that regard, this is likely more or less intentional. I'll leave this open pending confirmation.
Normally, only one add-on -- including XF -- can "own" a particular value for particular content and the last one imported "wins". We made an exception with BB code media sites so that if an add-on is providing a media site that XF can now handle, we won't automatically overwrite their version with ours (it may not necessarily be compatible). So in this case, when you upgraded, the existing custom handlers for this add-on would be maintained, but because the add-on is disabled, the embeds won't be available. You would need to install an updated version of the add-on (if available) or uninstall it, which should remove these records. That won't automatically import XF's, but it allows us to import them if you go to <url>/install/ and import the master data.
