I haven't been on Subeta since before the new achievement system rolled out. I looked around, went to the bug forum, etc... I have two questions:
So... any ideas?

The link to import has been removed but there is another link at the top of the achievements page to "process missing achievements." Another user who said they have not been online since the new achievement system was made said that this linked worked.
I'm fairly sure this will not cause you to lose your new achievements, since it is only processing the missing achievements. I think I clicked this after I had won new achievements and was safe. However I am not 100% sure. I still think your best bet would be to take note of the new plot achievements you earned, process the missing achievements, and if you lost any of the new ones make a ticket.
Good luck! :)