I am able to log into a standalone ESXi host using the non-web client and "Export OVF Template" as a single file.
Putting them back into Inventory may work out for you.
I used to make extra folders and extra copies of vmdk's in the datastores, but since none of them were ever added to Inventory, I could only see them when i browsed the datastore, which also caused confusion.
Don't be afraid to keep unused vm's in Inventory. They won't run if you don't want them to.