|Do you know where your variables are?|
Welcome to the monastery.
Firstly, a word about your data. The term list has a special meaning in Perl: see "perldata: List value constructors". I've taken what you've described as lists to be records in files. Given you wrote "... the 'names to be replaced' file ...", that seems correct for the second list; although, until I had read that far, I initially thought you might have been talking about a list of lists (which is something different — see perllol).
Anyway, this means you (probably) have a CSV (comma-separated values) file which is best read using a module like Text::CSV. The reason for this is that there are all sorts of gotchas with CSV files which have already been coded for in these modules. As an example, consider two records: "apples, red,cherries" and "apples, red cherries". If you had an ID for "apples, red", how would you handle the replacement in those two records.
So, I'd suggest you check whether your data really is as simple as the examples you've posted; and consider the chances of it staying that way in the future. You may need to revisit whatever solution you choose based on those findings. The solution I provide below assumes nothing more complex than what you currently show.
Here's my take on a solution. I create a hash mapping names to IDs (same as you). Next, I use the keys of that hash to create a regex with an alternation (e.g. bananas|oranges|...) such that only the names with IDs will be matched. Finally, the replacements are made and the new data is output.
Here's the files. Notice I added "pineapples", which didn't have an ID, and so wasn't replaced.