So I removed the back emblems and... surprise!

You basically have three choices. Either put the emblems (or new ones) back on, cover the holes with something else (like another emblem or sticker), or fill the holes and paint them.

 

I am a new owner and going through the same thing.. was not expecting holes!! Not a fan of the 3 Hybrid badges but do like the AWD-e.
I filled holes with white silicone, left a slight indent and filled with glazing putty.
Now it’s decision time.
Paint Blizz white OR put a different badge over? Easy to put back on if I need to.
I found a cool eBay TRD badge to replace the back right side. Probably paint the holes above the left AWD.
Hoping the front L &R fenders don’t have holes.
I will post the finished backside if I make a change.

 

Not judging but its kinda weird seeing a car without emblems in traffic, dont you think?

People are gonna think you are ashamed of driving a prius lol.

But to answer your question, you can try RTV to plug it then spot paint it with a $1 bottle of walmart paint in the crafts section or spraypaint, etc. Its small enough to where it shouldnt be very noticable. I once used gum, yes gum, as a plug a hole solution then painted it on top. Worked well and held for years till i sold it. Just gotta be creative