The decals in question will not show up on the livery but a ghost decal will be in its place, If you reupload the decal and then use replace decal on the correct ghost the positioning will remain the same so you can fix the livery so long as you can remeber what decal went where.
It wasn't the case in GTS interestingly, but somehow the liveries in GT7 refresh themselves all the time for whatever reason, and when decal x, y or z isn't on the GT server anymore it vanishes.
They should be stored in some of your folders on the iPad somewhere tho, depending on if you used that for uploading them as well and didn't deletem them there either