We didn't do anything but try to enter a quote. New quote number should have been 11478 and 9995 re-surfaced and now they are all following 9995. What happened and how do I get them back in sync? I have the duplicate invoice number/po number item checked in preferences.

Selecting the preference only creates a warning, it does not prevent you from recording the transaction by ignoring the warning.
The system, when selecting a number will go to the next available. If 9995 became available because it was deleted that is why the system brought that number up again.
To get the numbering system back to the 11478, use that number when you record the next quote ONLY AFTER you have changed the wrong numbers to the correct ones.