Agreed it's confusing.
I read it that the OP said that the last 3 chars of the filename will be different, the rest is unique. I assumed by that he meant that the directories have say in dest & src ….
foo00234 ~ foo00123
bar00567 ~ bar00456
and that he wanted to overwrite foo00234 in the dest directory with foo00123 from src, same for bar00567 ~ bar00456.
Yes, i didn't bother checking the contents if they match (i forgot that bit 😉 But if they do, it'll just use up a bit of disk bandwidth. An md5sum would be easy to add before the cp …