I don't think it will be a big deal to transcode MP3 to Opus as long as you're okay with for-sure having theoretically-scuffed-up audio files. Every time an encoder has a go at the files (especially different encoders) they'll leave little artifacting marks all over the waveforms, typically seen as little "blocks". Are they audible? Doubtful. If you want to keep a neat and high-quality library I'd recommend collecting FLAC next time around.

Also, this won't work on Win11, and I don't think you can make it transcode MP3, but if anyone happens to have slightly different requirements I'll plug https://gitlab.com/beep_street/mkopuslibrary, which I use to keep my FLAC library in sync with a parallel Opus library for mobile use.