I have the same issue with VSC 6.2 on vSphere VCSA 6.0.2 and 6.0.1. I called to open a ticket and the tcehnician acted like he had never heard if this issue before and asked that I pull logs from the VSC and vCenter web client. I will simply not be using the VSC plugin until they work this bug out. It is quite sad that this isnt a known issue and addressed as such based on the amount of the community members experiencing the problem.
I have downgraded to VSC 6.0 per Netapps tech support. This seems to be working for me. I would open a case with Netapp and they have some prep/cleanup steps you can follow before you install the downgraded version. Note: I am running Virtual Center appliance 6.0 Update 2. Netapp has not fully vetted out VSC 6.0 on VSCA 6.0 U2 but was the suggested work around and so far so good.
Installing VSC patch 6.2P1 also fixed my issue with hosts disappearing from vCenter. However, it seems to have introduced a new one. My hosts now randomly disconnect from vCenter. vCenter logs would indicated that there was an error with the host name in subject for the host certificate. I have verified the host cert and thumbprint as being correct. Since unregistering VSC from vCenter and shutting it down the random host disconnects have stopped. Has anyone else been experiencing this issue with VSC?
I have implemented VSC 6.2P1 and have not experienced any disappearing hosts anymore. I am now in the process of upgrading/installing the other components (VASA/SRA 3.0) to get my VMware SRM environment active again.