Is is possible to install multiple copies of Eclipse/Atelier, and have each instance maintain it's own distinct list of server connections? I thought I had figured it out, uninstalled everything, and reinstalled without using bundle pools. I think this keeps projects separate, along with allowing different Eclipse settings and plug-ins. After installing the second instance, no server connections from the first were showing in the second. I added connections to the second instance, and after closing Eclipse and opening the first instance, that instance was showing the second instances connections, not the ones I had setup for that instance.
Your Atelier server connection information is stored in Eclipse's secure storage file. The secure storage file is shared among different workspaces created in the same Eclipse client. You can see the location of this file in your Eclipse preferences under General > Security > Secure Storage > Contents > Storage location.
The location of the secure storage file depends on the directory in which Eclipse was installed. If you want a second install with an independent list of server connections, you will need to install the second Eclipse client in a new directory.