Hi @johnywhy,
WP Migrate Support Team here. Thanks for reaching out with your query, we would be happy to assist!
Even though you can exclude users when exporting a database, you might not be able to avoid overwriting users on the destination site. What you’re describing sounds like ‘database merging’.
Merging databases is a tough problem which WP Migrate doesn’t support. WP Migrate replaces database tables at the migration destination.
Something our team has done in the past is use production as the ‘master’ database and pulled in changes to the dev/staging environment they’ve been made.
Another option is keeping track of the changes you’ve made in dev/stage and manually applying them to production.
Iain wrote about how to merge data with custom ‘migration scripts’. These are essentially code level changes that instruct the database how to change.
https://deliciousbrains.com/syncing-wordpress-database-changes-merging/
As I mentioned, it’s a tough problem and many other WordPress developers are also battling this issue.