It's fine to have both .cia and .3dsx freeshops. It's also okay to have one freeshop injected in Health & Safety through GodMode9 and another with its standalone CIA. Now, if you have two freeshops on HOME Menu, that's NOT cool. One of them is the odd one out.
You didn't happen to install any other freeshop .cia except for the v.4.1.3 listed
here?
Go to FBI and look under
Titles. Find the one that has the Title ID of
000400000F12EE00. This is the one you want to keep and it should be listed with it's named highlighted
green. If you see one listed in
red, leave that one alone too as that's GodMode9 injected. If you see another freeShop that does not have that Title ID, use
Delete Title and Ticket to remove it.