Problem Reported
User email notifications no longer send with the “Send notification email” option checked

Recent Change (Routine)
A Create & Update flow was added with an Update Record element at the end. Standard Salesforce functionality, very normal, nothing crazy here.
Troubleshooting
This was a process to discover a Salesforce bug:
- Checked Debug Log
- No errors
- Checked Email Log
- Emails not being created if the new flow was activated
- Deactivated new flow
- Fixed the email problem but eliminated the new requested updated to automation
- Incrementally removed portions of the flow to identify a specific cause
- NO EMAIL until the Update Record element was removed
- The Update Record element is needed to apply the flow updates. THAT WON’T WORK!
- NO EMAIL until the Update Record element was removed
- Created a simple flow that had only an Update Record element
- NO EMAIL
- Created a simple flow that had only an Update Record element on a different object
- NO EMAIL
- Created a simple flow that had only an Update Record element on a different totally new custom object
- NO EMAIL

Conclusion
Salesforce has a bug that prevents user change emails if there is a flow that runs a User Update Record if the record’s Owner ID is changed and Owner ID changes are not ignored.
Work-Around
Ignore Owner ID changes. Set the entry conditions to avoid running when the Owner ID changes. This can be done through a Decision element as well.

This is not ideal, but for the customer it was an acceptable work-around.