For the last couple of time that I updated, the naming series I created for some DocType such as Journal Entry, Sales Invoice and Purchase Invoice always disappear.
Even I have faced this issue a couple of times, I was wondering where did the naming series vanished.
I had defined custom naming series in Sales Invoice and one of my custom doctype which were not there after I ran bench update / bench migrate. I am on ERPNext: v8.0.33 (master)
Are the customizations stored in a repository? Or is there a repository linked to your current project?
What we usually do is we run export-fixtures so that naming series, custom scripts, print formats are also stored in the custom app repository and can be pushed to the rep. We pull the changes from the repository, and run bench migrate. If you have a database backup with the recent changes, you can also try restoring the db.
Can one of the developers who has naming series working run export-fixtures and then push the updated file to your repository? Afterwards, you can update your instance and then run bench migrate.