If you go in the factorio mods folder you'll find the zip files of all mods you downloaded.

• Decompress the mod you want to change,
• Delete the original zip file.
• Edit the files freely.
• Factorio will load the mod as if it was coming from the mod portal. You have to restart factorio at every code change.

Don't post it on the changed mods on the mod portal though! And do check the mod license on what you are legally allowed to do with it, becauss some don't allow derivative work or changes, including fixes (even though if you keep it for your own personal use this is a bit less important, since nobody can know what you did)

If you feel the changes are small and purely for compatibility you can try to contribute it back, but do always ask the original author, and respect a "no" :) !