Some devices suddenly gone offline yesterday. And our presence sense virtual switches disappeared

most likely, they have already been migrated to Edge drivers and you simply need to switch to a community developed Edge driver. In most cases, you would not need to remove and add back.

FAQ: What is Edge

Legacy Virtual devices stopped working

for virtual devices… I would recommend use this Edge driver to create new virtual devices: https://community.smartthings.com/t/st-edge-vedge-creator-a-virtual-device-generator-for-end-users/231786

for the other devices that are offline… if you can provide brand/model for them, we can provide better advice for getting them to work for you.