We do on a mold remediation, unless it was small, you don't want to risk failing a IH test because of a used HEPA.
For WDR, Sheet rock dust cleanup, fire damage, rarely unless we are talking about extended use.
The job usually doesn't required us to replace the HEPA, but I'd charge off the primary and secondary filter.
If it's anything nasty I wouldn't risk it, I'd charge it off and replace it.