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Simple question, is there any way to restore Pase so that for example QOpenSys/ restores all files back to scratch ?

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You might be able to uninstall the licensed program (5761SS1 opt 33 in IBM i 6.1) and then re-install. I haven't tried it but I would think that would get you back to basics. The only issue would be if you have added other PASE programs to your PATH and altered the PATH then those programs might still get executed rather than the 'vanilla' PASE programs

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