A hack approach seems to be possible via manually editing the first two lines of the .prj file. To be backwards compatible, it should start as follows:
<deployment-project plugin="plugin.matlabcoder" plugin-version="R2015a">
<configuration build-checksum="..." file="..." location="..." name="..." target="target.matlab.coder" target-name="MEX, C, and C++ Code Generation">
where the ... should be left as they were.
The changes are the renamed plugin (from "plugin.coder"), the renamed target (from "target.unifiedcoder") and the renamed target-name (from "MATLAB Coder").