I have exactly the same problem, same CodeWarrior version 5.9.0.
Also working w assembler absolute code.
On a S12E64 mpu though but that should not matter.
If I copy back all files from my safetybackup, it works nicely.
The sourcecode appears nicely in the debugger.
But as soon as I want to change the sourcecode to another file
(by "remove file from project" and "add file to project")
(as I have done hundred of times before, and it still works on other projects in subdirectories parallell to this one)
then the "Enable debugger for target "Standard" window appear.
No matter what I select Yes/No/Cancel the debugger starts with sourcecode missing.
PLEASE SOMEONE HELP !
I dont want to have to create a complete new project everytime I am updating/changing back a version of my code.