The Precursor Studies Center does not replace the Precursor Engineering Center, but instead is buildable in addition to the Precursor Engineering Center. This is because the UpgradesFrom for both is the XenoArcheologyInstituteModule. The UpgradesFrom for the Precursor Studies Center should be PrecursorEngineeringCenter.
The fix is to replace the line:
<UpgradesFrom>XenoArcheologyInstituteModule</UpgradesFrom>
for the PrecursorStudiesCenterModule in the StarbaseModuleDefs.xml file, with:
<UpgradesFrom>PrecursorEngineeringCenter</UpgradesFrom>
