dave, not sure this will help......but here is what i do.....
i harvest once a year. i will be taking my supers off this weekend, all of them, and with goldenrod. i have done checks to see what is capped and not. late summer, the bees can 'lose interest' in capping what they are doing.....
best and short way i can describe it, or under other circumstances. your bees are probably not going to cap anything left on. that's just what i think. they just get to a point and quit capping. they may fill frames, and cap a little.......but not the rest.
when i extract, i stack the boxes and pull frames from them, uncap, and sometimes the frames get mixed to balance the extractor. if i have frames that are not capped or fully capped, i usually follow the old rule of how much is capped and do a shake test.......if anything flys out it goes back to feed the bees. if i have some late frames that are 1/2 to 3/4 capped, shake test and nothing flys out, i will mix two of these frames in for every 9.........i have a 9 frame extractor, so two of these not fully capped frames go in with the fully capped ones. i don't have a refractometer....., maybe someday i should invest in one............
some beeks say they are comfortable with adding frames that are not fully capped with a little flying out to mix in with fully capped frames. i guess it depends.
if you mix a frame or two of goldenrod into the rest of your honey as you are extracting it's not going to matter. goldenrod does crystalize quicker, but does have a great flavor, that's just my humble opinion. if you have full boxes of goldenrod, just mix them up with the rest of the frames as you are extracting.
also, like keith said, the bees when they collect honey, honeys really are stored 'separately'....i will have boxes of different blooms as everyone else does and as you do. with certain blooms i want to harvest separately, i will mark the box of what i think they are collecting as well as with comb honey; i usually know or have an idea of what the honey is from, from the bloom time of the plant they are visiting as the boxes are filled. i super bottom to top and i don't move around.
goldenrod does have a sparkly smell to it on the hives............
but once harvested, it's good honey!