The short answer is YES... I run two instances of Amibroker for real time day trading (I don't do backtesting)...
I have a lot of info being processed live and I have 3 monitors with 12 charts on them. I simply cannot run it all in one instance of Amibroker... So I run two... I do the same. I use small files to share info when I need to. It's not ideal... What I'd really like is AB to support multiple core processors... but running separate instances will definitely utilise multiple cores and increasing your access to processing power.