If the design entry is schematic, I click on I/O Pins "Design Browser"; wrong pin names are displayed, and if I select-drag-release any of them on the "Device Architecture" window and Save, the UCF file created makes NGDBuild fail:
Annotating constraints to design from file "uuu.ucf" ...
ERROR:NgdBuild:755 - Line 6 in 'uuu.ucf': Could not find net(s) 'A0' in the
design. To suppress this error specify the correct net name or remove the
constraint. The 'Ignore I\O constraints on Invalid Object Names' property
can also be set ( -aul switch for command line users).
This is a known issue and will be fixed in the future.
To work around the problem, input constraints in ucf.