I was patching a lot of ESXi hosts but had some trouble with one of the clusters. Remediation did not work and in the Events for the first host I saw two events:
Could not install patches on <host name>
Remediation did not succeed for <host name>

A quick search on the WWW learned me that the packages folder could be corrupt. And indeed, it was… So how to solve this issue?

The first step is to get the volume where the store is linked to. If necessary, enable SSH on the host (Configure/Services) and log in to the host. Then enter the following command:

ls -ltrh / | grep store

This will give you output similar to this:

Save the path for store and lookup the disk where this volume is stored:

vmkfstools -P /vmfs/volume/5f6afaf1-664876a5-0f57-000c29acef63

In the above screenshot, the disk is mpx.vmhba1:C0:T0:L0:8. Now format this disk. PLEASE MAKE SURE YOU SELECT THE CORRECT DISK

vmkfstools -C vfat /dev/disks/mpx.vmhba1:C0:T0:L0:8

With the new volume created, delete, and recreate the symbolic link. Remember to use the new volume!

rm /store
ls -snf /vmfs/volumes/5f6efbe4-e4ceac0e-5a06-000c29acef63 /store

The last step is to copy the content of the store folder from another host. You could use WinSCP for that.