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Are the files in the error message related to encrypted IP source files? In 8.1 and lower, Quartus II would look for the source encrypted IP files to find the license info for the IP. The license info would be required to generate a .sof, since IP doesn't support programming unless it is licensed.
In 9.0 the search for Ip source files shouldn't happen, so you could try in recently-released version 9.0 if you think this might be the problem...
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Yes, the sub-compiled partition is encrypted source files. I'll run it on 9.0 ans see if teh problem persists.
thanks