Catch 22.
On the one hand you loosen the compression on the insulation, on the other hand the hanger is helping support the stretch on the flex, taking pressure off the 2 ends. With the flex just laying on the hangers the compression is limited to bottom only but there is nothing helping with the stretch so the flex will pull hard on the 2 attachment points one on the duct the other at the boot. These are supposed to be taped and screwed but even at that the flex liner can unravel whether screwed or not.
Personally I would leave it. If you are concerned about energy lose then wrap some extra insulation around it at those points.