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Check the new 'tag migration' system under services->review services. I assume the tags are under 'my tags', right? Go to that services panel on review services and then hit 'tag migration'. That'll let you export all current tags to a Hydrus Tag Archive. You can do the same on the other end to import to your 'my tags'.
For the videos that failed, what's your FFMPEG version under help->about. For the Linux release of hydrus, it uses whatever your OS has. If it is old (I think current version on Windows is 4.1 or so), try updating it on the system level or putting a static built executable under hydrus's install_dir/bin. There should be a readme there explaining the situation as well.
Otherwise, do you have any of the error traceback 'notes' for the failed video imports? This might help figure out what went wrong. Click the little icon button on the importer that failed and find the import row that failed and then right-click->copy notes.