My favourite in Spanish (but I think English speakers can relate) is "botica" (pharmacy) and "bodega" (cellar), both from Greek apotheke (basement, literally "under-box")
Some I can think of offhand are the ones with the consonant + l -> ll change:
Plano + llano
Clave + llave
Pleno + lleno
I think there are some others where Latin vowels like /o/ or /e/ change to diphthongs like /we/ or /je/ and they get re-imported with /o/ or /e/ again. I can't think of examples of this right now but I am sure they exist. [Edit: foco + fuego is one such example]
Probably others with word initial /f/ put to silent h, then re-imported with an f again.
Wiktionary has a long list of these here:
https://en.m.wiktionary.org/w/index.php?title=Category:Spani...
As dt_r pointed, apotheke always meant "away room" so it makes sense to think that it got the new meaning because of context: it surely was imported alongside other Greek terms about drugs.
Actually, "apo" has the meaning of "away" here, so "away-box" would be more accurate. Maybe you are confusing it with "ypo", which actually means "under" in Greek?
I always enjoy reading about this stuff, btw!
Anything with the "teca" (or "theque" in other languages) has some relation, like modern discoteca or biblioteca = library.