I'm sorry, I'm not very clear. I got help from Ken Task (THANK YOU KEN!)
who went ahead and deleted them. Let me explain:
I had moodle 2.3 installed on production server. Then I upgraded to Moodle 2.5 but kept the old database of classes etc. When logging in, under administration/plugins/admin tools/ manage admin tools or in browser just moodle/admin/tools.php
I saw 2 tools said they were missing yet at the same time it had on the far right a delete button for those who wish to uninstall them.
These two tools WERE in my server folder under admin/tools in 2.3 but NOT inside the same folder in 2.5 meaning moodle changed that unless I somehow added them myself to my last system.
The database recognized the tools were once there. Amazingly, even though they were gone from the physical new location on the server in 2.5, Moodle still let us 'delete' the ghost of them in admin.php likely because it removed that from the database. All is well so far . . .
It was weird I know, but I thought I would share the solution just because others may have this happen and it was a surprising cause and solution for me. Thanks again Ken and thank you too Howard for asking me to make it clearer. Moodle is the best place!