Yeah, I read this on a brake forum:
Disconnect all the lines and flush with denatured alchohol useing a rubber tipped syringe. If you rebuild, rather than replace components, also clean them with alchohol. Once the lines are disconnected at both ends, the alchohol should flow freely. If there is an obstruction, use compressed air. Do not use compressed air with components still attached. Sometimes rubber parts can seem to survive something like this, only to go bad later, including the flex lines, if they have been infected. I have gone the cheap/easy way before, if i believed the contamination was isolated to the master, and just replaced a contaminated master cyl, then back flushed the lines with new fluid via a syringe thru the caliper bleeders with the master removed, and not had a problem. but if you believe the contamination has made it's way to the calipers, or have any doubts, all rubber must be replaced, all metal must be flushed with alchohol. On a personal note: I was not aware that a dot 5 and 3 (or 4) mix would swell seals. I knew they were not to be used together, but assumed they just did not intermingle. it is good to know.

Sounds like anything rubber has to be rebuilt/replaced, including flex lines. Bummer!