I encountered this SAME problem. I wanted an installshield project to run another installshield project (which was an updater) to bring the software up to date before installing the first installer.
I solved this by creating a batch file.
1) The user launches the install msi.
2) The installer prerequisites detects that "previous version must be installed" by checking the registry and runs the batch file
3) The batch file kills the current process of installer and runs the second installer
4) Once the second installer is finished, the batch file re-runs the first installer (by using the batch command START /WAIT, which waits for a process to finish)
5) Now that the second installer was installed, the prerequisites doesn't trigger, and you resume with the installation.