Springtime, what’s next?

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Ok I have a two part question: First off we had a very active hive last year and I’m proud to say they seem to have made it through the winter. The first problem we had the bees never made any honey in the “super” but they were definitely in there but never seemed to cap. So in the fall when they moved to the lower two boxes we removed the “super” away. The lower two boxes however were filled with honey combs. Now that we are approaching spring the bees are getting active again but I’m not sure what I should do with the frames that had the honey (again these were packed). Should I take them out and clean the frames up and reuse? Leave them add another box? and when should I add the “super” again…. and why didn’t they cap it, we aren’t sure what our next step should be. Please Help!