Our collector service is completely unaware of SCOM agent, it will do its job regardless of agent version or even without SCOM agent. However without agent or right after reinstalling the agent you will loose topology objects which were being collected by this collector server. In case of re-installing agent, the topology will be re-discovered again.
If it's OK that objects monitored by this collector will disappear in SCOM and then appear again, then you can do agent re-install without doing anything with collector.
To avoid VMware objects downtime, you can do the following:
1. Relocate monitoring jobs from this collector to other collector(s), you can deploy a temporary collector if necessary.
2. Wait some time, so that topology objects are discovered by other collector(s).
3. Reinstall SCOM agent.
4. Check that proxy is enabled on re-intalled agent and run "Configure OpsMgr Agent" task.
4. Wait for re-installed agent to re-discover collector.
5. Relocate monitoring jobs back to collector with re-installed agent.
Hope this helps. Thanks.
Feel free to ask any other questions.