Actually, the issue is that some injected yokai wont appear in the game regardless if you gave them nicknames or not, and it may even erase some that you already own (it happened to me when trying to add a non-nicknamed Swelterrier and Eterna, not only they didnt appear in my savefile but it also made my Uber Geeko and Arachnevil dissapear into thin air) its more safe if you just replace yokai you dont need with the new ones.
The same issue happens to the items, replacing items seem just fine, but adding new ones on empty slots seem to make other stuff dissapear, like key items for example.
I didn't add in items. As far as the yokai you had disappearing, did you do the number conventions that yokai watch uses for the items and yokai? I'll do a test on the two yokai you tried to inject and see if weird things happen or not
Edit: It took me a couple of tries but I was able to get the two yokai that you mentioned to properly appear as new yokai (Not replacing old ones)
The steps are:
1. Selecting an empty slot
2. Selecting the Yokai you want from the drop down
3. Setting the level (Do not leave it at 0)
4. Click the Default button under the Technic dropdowns
5. Setting the IS_NEW and Special Flags
6. Clicking Auto-Number and hitting Yes
7. Clicking Update ID and hitting Yes
8. Clicking Fix IVs and hitting Yes
9. Hitting the update Yo-kai index button. Ignore the message it says as this is a necessary step (Also it's not Yokai Watch 3) and hit yes again.
10. Hit Apply so it saves the information (You have to do this before selecting another Yokai slot or going to another tab)
11. Go to the Yokai Medallium tab and check both the seen and befriended boxes for the yokai you're adding in.
12. Hit Apply here too.
13. Save and you're done.
I still haven't done anything with items yet but you probably have to follow the same conventions with items as yokai. The battle items in particular already have the #1s set so you probably just have to do the auto number for the item you're replacing or adding there.