Can I cook my cranberry sauce longer to get it to thicken after it has cooled?
What is in your recipe? I finely dice an apple and add it to the sauce as a thickener. Works like a charm. The sauce will be a bit loose when hot and thickens more as it cools.
This won't help in your current conundrum, but if you have a super power blender (like a Vitamix), you can blitz your cranberry sauce with the skins on and it will set up perfectly. You won't get the perfectly clear sauce but it is still a beautiful shade of red and it will taste just fine.