If you manually add the '}ElementAttributes_Assumption Inputs' cube reference to the application tree, you can see that what will be added is a '}ElementAttributes_Assumption Inputs.cube' reference. This then is the label of a file with that name in the '}Applications\Models\02 Count\02 Dimensions\Control Cubes' folder in the TM1 database directory describing the linked object.
So, in other words, the link is indirect and cannot be added in the way you're trying to do this currently.
An ApplicationsAdd function would be helpful here...
I found a work around, Looking at your .cube short cut file found on the server i recreated the shortcut inside of Excel, then using a list of Cubes and Dimensions on another sheet created a looping macro to create all my .cub .dim .proc shortcuts and got the macro to save them to my main folder.
from there i transfered these files into the application folder of my choice manually,
I then ran the same TI as below with the correct names of the shortcuts in, it did not need the .cub/dim/proc ending and i would like to point out that when the TI ran regardless of what my Vconsol was set to it still sat outside the hierarchy, once the server had been restarted the shortcuts showed in the application entries in the correct folder of the shortcuts. i put the shortcuts into a diffrent location to my Vconsol and found they still linked up to the correct folders regardless.
this sounds alittle long winded i know but its a three step process that takes 2 minutes to run, i found that just grabbing and dropping the required Ti's, Cubes, Dimensions was taking hours especially if the server was heavily loaded with models. if anyones interested in the excel sheet send me a private message will be glad to email it on if needed.
thanks anyway for your help guys, if anyone can find a quicker solution please feel free to add it here..