This warning tells you that you may be doing something wrong. If you are creating your second version and intend to distribute it as a minor update or, especially, as a patch, consider accepting the warning.
Patches are created by creating two .msi files and then using the Patch Design view to turn their changes into a .msp file. Some things, such as dynamic file links, increase the likelihood that two .msi files will be thinly incompatible; The Patch Optimization setting helps reduce the likelihood of such incompatibilities by providing InstallShield access to the layout of the previous .msi file. Since InstallShield cannot predict whether you will create a patch later, it warns when creating the main .msi file.
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