EndNote™ was not designed or tested for Terminal services, Citrix (including Citrix App-V) or Microsoft Evergreen and we cannot provide direct support for this configuration.
We have spoken with users who have been able to run EndNote in a Terminal Server/Citrix/Evergreen environment. In this environment everything runs from the server and the computer thinks it is a dumb terminal, i.e. it is not aware of its local resources. The attractive feature of this environment is that it can allow older and lower-power computers to run some of the newer Windows programs that they would not be able to run in the standalone environment. Every file and setting that would exist on a normal workstation would have an analogous location on the server under Terminal Server/Citrix/Evergreen.
If the user is familiar with his/her system it would be possible to copy the appropriate files to the proper location on the server and make everything work correctly. However this is not something for which we can provide direct support.
Extra info
VDI (Virtual Desktop Infrastructure) vs. Terminal Services (or RDS) debate is based on the differences between the two methods for delivering remote desktops. One uses sessions and the other connects users to full client OS desktops.