I recently did a software update deployment, and yesterday we had a lot of compliant computers.

This morning I checked, and 99 percent of them are showing unknown compliance in category Client Check Passed/Active

Any idea what would have caused this? Will running a summarization bring this information in again?

A change in the deployment compliance is usually caused by a re-evaluation of the software update deployment. This is configured in the client settings. That's also the reason why you should use the reports for checking compliance of software updates.

The compliance is based on the current deployment. If you add / remove software updates from the deployment group, the compliance checker will reset and rerun to ensure that the devices are complaint with the change.