That's another odd situation. Edit the item. Change its ID to something unique (80001 or something). Add the correct ID. Now you'll have two copies of the item. Mark the specific enchanting of the the first one, and the specific enchanting of the 2nd one.
Might it be an idea for us to add a routine that runs on starting optimise, similar to the "you have a lot of X it might take a while" check, this routine would check weapons and if you have selected a non-unique one-hander as available it asks
if you have one or two of them and sets a flag appropriately?
On the two the same different enchants - surely if the optimiser is working out that you should use the same enchant on both then the one that changed was sub-optimal?