Changing the hostname should not affect an existing site-site IPsec VPN. It will not overwrite any existing pre-shared key. It won't change any RSA key or keys (even though that's not used in a VPN) that are existing.
The only way I can think it would affect the VPN would be if you were doing something like using the device FQDN in the identity (e.g., with FlexVPN) and you were changing the FQDN as part of the hostname change. However that is a very uncommon use case.
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