hi
I understand that (anyone correct me, if i am wrong), when we delete atoms in VESTA manually, then it only visually 'deletes' but not physically from the model. It's not a bug, but designed like this.
if we want to view after deletion, a roundabout procedure is there, i think. [ I read or heard somewhere or from someone.]
1. delete the atoms whichever you want.
2. convert the file as .xyz format and save it
3. reopen it and then convert again to .cif
I remember trying this procedure, but I don't remember whether it was successful or not. Because I have not used VESTA for such editing :)
you can try and check, Let us know if successful.
Regards