I would open and save both subprojects separately in the software version you are currently using to merge the files. This should make sure that they have the same version of the .p4d file afterwards. It could happen for example that the software was updated after having created the subprojects and then it throws this error, because the versions of the .p4d files do not correspond with the software version.
I’d also make sure that the coordinate systems are set the same in both subprojects. More about merging in this article: https://support.pix4d.com/hc/en-us/articles/202558529
Let us know how it went! If it didn’t work, let us know more about what version you are using.