Hi Alex,
In general, I would not suggest deleting Software Resources unless you know nothing is using them. I've deleted things before, though, without problems.
You can select two Software Resources in the Catalog and right-click them, then choose to merge them. Or select one of them and right-click it, then go to the Actions menu, and you'll find a "Resolve Duplicate Software Resources" option that helps you pick which item to merge, and gives you an option to reassign the resource identifiers of computers with that resource, so you don't have an orphaned references.
I hope this helps!