Even if it is 6 Month ago - I'll post my advice here (instead of opening a new topic):
Just rename the .iso to .bin and edit the .cue file to match the new filename of the renamed track (Works in RetroPie 4.1 with both lr-* emulators).
Keep in mind: changing the file extension does NOT convert the iso to a bin file, it still is containertype iso just renamed to bin... wait, Just tried, you can change the extension to "anything", as an example .!iso won't be shown by ES but still be loaded if referenced in the .cue (And with such a file-extension one will be reminded that it is a track in iso format) ;)
If the scraped information was associated with the .cue everything should be fine, if it was scraped for the .iso I am not sure (There are some scraping issues for the amiga and the using of .uae files instead of .adfs thats ringing a bell in this context) - sorry, haven't done a complete scraping run yet - just tried it out with selecting cd-title (.cue) -> edit metadata -> scrap, and that worked fine...