“because internal PC’s are affected (routed trough A or B link) by NetBalancer.”
This is the nature of netbalancer/load balancing. Your LAN will utilize both of your ISP connections based on the metrics you configured for netbalancer.
It seems that your LAN is experiencing undesired routing because of netbalancer and your vpn clients are experiencing intermittent access to LAN resources because netbalancer is enabled. Disable it temporarily and test your implementation for the desired outcome.