If you are forking an extension but not renaming the columns, make sure you migrate down the original extension before running the migrations of the fork (select "Uninstall" in admin panel next to old extension).
Or you can rename the columns to have unique names that won't conflict with the original extension.
Or you can modify the migrations so that they ignore existing columns (but there's some risk of errors on migrate down if the migrations don't check the columns exist before deleting them, the inverse problem)
The migration history is based on extension ID + migration name, so even if the migrations have the same name as migrations that have already run, if your extension has a different extension ID (package name) Flarum will consider those brand new migrations.