What Axe firmware are you on? What operating system on your PC or Mac?
When using Axe Manage: After you coy or import an IR into an AE Manage user slot do you then highlight the user slot, right click, click on Send To Axe Fx, then click on Selected Cab or Changes Only? Just moving cabs in Axe Manage isn't enough, you have to send the new IRs and/or locations to the Axe.
The middle User Cab column in Axe Manage shows the cab in the Axe, the first column is what's loaded in Axe Manage and the third column is the IR file in the Axe Fx/cabs directory in Axe Edit's workspace - it can be confusing as each of the 3 User Cab columns could be pointing to a different IR when, intuitively, one would expect all 3 columns to reference what is in the Axe Fx.
If it doesn't work have you tried quitting then restarting Axe Edit, restarting Axe Edit seems to fix things (temporarily) when I Get a cab from the Axe to Axe Manage then Export but end up with an unusable file. Sometimes an existing file with the same name in workspace/Axe Fx/cabs has to be deleted before Get Cab From Axe Fx will successfully retrieve and locally save the IR.
With all the excitement over IRs, and all the money I've recently spent on mics and pres, it'll be great to have Axe Edit working smoothly.