You need to be more specific with what works and doesn't as well as what the VPN solution is.
If LAN-to-LAN and LAN-to-PSTN both work without issue but inter-site calls (which must cross a VPN tunnel) get no audio, then this isn't a VoIP issue but a route or firewall issue. For example, protocol inspection may be interfering with the SCCP/SIP headers. Another possibility is that the VPN headend isn't allowing traffic between the source/destination subnets.