>>262 if you can keep them separated in your head then it's pretty much just like learning one more reading for the same character/word.
i know the chinese readings of a handful of the most common characters in mandarin that are also used in japanese and it doesn't really mess me up, on the contrary i think it helps mentally cement that character as a semantic unit. it's like if you learned spanish, then learned italian, then found some word that's cognate between both languages that both have an ultimate origin in the same latin word, it helps your total understanding rather than hinders it.