This article explains how to remove ESXi host from vSAN Cluster with File Services enabled.
VMware vSAN
1. Run pre-check for host maintenance mode with full data migration.
2. vSAN file service VM may start showing inaccessible.
This inaccessible VM is part of a vSAN File Service deployment, and its vdisks are stateless. During a full data migration of the ESXi hosts, the vSAN objects for shares will be automatically migrated to the other hosts, but there is no need to migrate vSAN file service node.
Once the host is placed into maintenance mode, this VM will become inaccessible because it is using a Storage Policy with no data redundancy (the default FSVM Profile DO NOT MODIFY policy). Typically, this VM should be removed automatically from the inventory once the host enters maintenance mode. If that does not occur, it can be safely removed from the inventory manually.
3. Once this is understood, the user should follow the instructions as described in Permanently Decommissioning a node from a vSAN Cluster.