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Neither ninja nor msbuild are compilers, instead they are "build" processors that call on compilers and linkers to process the source files and produce the build artefacts.

If both builds are using the same compilation toolchain. e.g. MSVC, then it's likely to work. Combinations of toolchains might not. I guess you'll have to test it.

Out of interest, what plugin is using ninja for its build system?