I don't understand how the water got trapped in there after you drained the system, removed the filter, dumped the water, and reinstalled the canister.
Anyway, since it is there, you have 2 choices:
1) Drain the RV antifreeze using the low point drain into a RV antifreeze jug. Remove and dump the liquid in the canister and reinstall. You should not need to replace the antifreeze since any fresh water has already been displaced in the initial flush.
2) Do Nothing. Over time the water will mix with the antifreeze, diluting the antifreeze only slightly as it tries to reach equilibrium. The reason they are separated currently is the lower density of the antifreeze is sitting on top of the water like a shot of Dark Rum floater on a Mai Tai.
Over time (left to itself) that drink will assume a uniform color.
Lou and Laura with Bella - German Short Hair Pointer
2008 GMC Sierra 2500HD Crewcab SB Allison Duramax
2010 Flagstaff 8526RLWS - Superglide 3300
HAM CALLSIGN - KC3FFW