So sorry about the delay on this; work has been hectic and this got lost in the chaos.
As of writing I haven’t published it to the plugin repo yet, but I’ve just finished reworking the file management system to solve your issue.
Edited files are now stored in a separate directory in wp-content, and will be loaded in place of their originals provided they are newer. This way updating a theme/plugin won’t break your edits, however, after updating you’ll want to check if there were changes to the original translation files and replicate them as needed on the edited version.
Basically, the recommended workflow is you update the theme/plugin, see the notification, click the link to edit the file, which now includes a link to the original, and once you update/re-save the edited version, it’ll take over again.
I hope this helps. There’s also some comment editing capabilities that I was working on earlier included in this update.
https://github.com/dougwollison/pomo-editor/releases/tag/v1.2