Probably the names are not wrong as such, they are just old names that you have had. The name is a library/index to start quickly something that you have used before - it will not get cleared up, it the drive still exists (or perhaps the directory, too, has to exist). Drive - if we talk about a Windows host.
You need to manually delete entries, which are not valid anymore and leave only the one that you actually have left. Not sure how you use VMware, but the logical way is to have one VM = one folder. If you do so, it is easy to manually know which entries to delete. I always use the virtual computer name the same as the folder name (if the creation goes wrong, you can always change either of them).
If in doubt, delete them all from library (NOT from disk, select carefully) and start the one that exists by browsing to the correct folder and VM computer. Then you only have one in the list.
... there is also another scenario, which will lead to multiple entries. If you copy your VMs (within your same physical system), by copying the VM-folder, AND then say, when first opening the new copy "I moved it", it will create a duplicate index, because you just told VMware that this is the same as the previous one. In a copy-VM case, you do need to do manual cleanup of those library indexes, rename the other VM for your own clarity and only then let VMware to add that entry to the library index with the new name.
VMware does not care what your VM computer vmware-name is, but you need to keep it logical for you own sake. Thus one VM = one folder AND VM name = folder name.