I'm sure it can be handled. Will armory work as is or do you know it won't?
For reference, when I did the upgrade from RAM-only to LevelDB-backed databases, I designed the DB build&scan operations to accommodate out of order blocks in the blk*.dat files. Basically because I heard murmurings of this change coming more than a year ago.
However, I never actually tested it and there might be something stupid preventing it from working, but it should be a
very short upgrade path to make it work.
In the future, I'd like to get away from blk*.dat files altogether and just pull things over P2P from your localhost Core instance. If you do that, you can guarantee you get them in order, though there other nice benefits (like no longer even having to specify a --satoshi-datadir, and being able to use a single trusted Core instance on a network for a bunch of Armory instances).