I think your setup is this way:
AutoVPN to the other sites
VLAN interfaces on the MX needed for inter-VLAN routing
VLAN interfaces configured with VPN enabled in the AutoVPN configuration
The new setup:
Delete the VLAN interfaces on the MX
Configure a transit-VLAN between MX and MS
Configure VLAN interfaces on the MS
Set static routes to the networks behind the MS. Gateway is the L3 interface for the transit-VLAN.
Configure the appropriate VLANs as VPN enabled