Yes you may run multiple instance of Starfish on one machine. You will do so by installing multiple Engines - that way you can deploy a different map/project to each engine. However, this will require care when using the Starfish Admin, because you must now chose or change which Engine you want to work with when you go into the application. You will also have to configure the Scheduler to work with multiple Engines.
However I'd also like to mention that we've made huge improvements to our platform in our cloud-based (IPaaS) Starfish Designer. Under a single login, it allows for multiple projects, multiple schedules, and requires no fussing about with engines and config files. It is the ideal location for partners/teams like yours to do ongoing integrations and migration development.
I also see you're running on version 4.1. Our current Windows version is 5.2 - however 5.x went to 64-bit only. Are you still on 4.1 because you needed 32-bit support? If that is the case, in our cloud platform we do offer Starfish Ray in both 32-bit and 64-bit versions. This will allow you to do cloud integrations with legacy on-premise applications.
I know of at least one customer that has multiple people RDP into a single Starfish server and run jobs at the same time. They have not run into issues though they are on a newer version of Starfish.
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