Resolving constraint associations...
Checking Constraint Associations...
ERROR:ConstraintSystem:59 - Constraint
"pcie_inst/pcie/BU2/U0/pcie_ep0/pcie_blk/clocking_i/clkout0" not found.
Please verify that:
1. The specified design element actually exists in the original design.
2. The specified object is spelled correctly in the constraint source file.
This error is due to the fact that I have constraints that refer to objects that no longer exist in the code. This makes sense since I commented out all pcie code. This doesn't make sense since I also commented out (from the project's UCF file) all constraints (including the above one) that refer to pcie code. So why is it complaining about a constraint that doesn't exist? After attempting my "Rerun All" commands, and after many changes and frustrations I discovered that ISE copies constraints from the project's UCF file into a PCF file during the compilation process. Since I previously had these constraints and compiled with them, the old PCF file wasn't updated. ISE doesn't bother deleting or recreating this file when manually editing the UCF file which causes it to give errors on constraints that no longer exist.
Delete this file, it might help.