In general, separating the prints from the frames is fine, so long as you document everything and assign numbers in a way that allows you to keep them associated in your records. Your decision has improved the storage condition of the collection.
Keeping works of art on paper framed is also acceptable, as long as the storage minimizes light and the frames aren’t damaging the works – but yours were.
Here’s a helpful leaflet on matting and framing for works of art on paper: https://www.nedcc.org/free-resources/preservation-leaflets/4.-storage-and-handling/4.10-matting-and-framing-for-art-and-artifacts-on-paper
I hope this helps, please feel free to post any follow-up questions.