This warning is telling you that you might be doing something wrong. If you are building your second version and you intend to distribute it as a minor upgrade or especially as a patch, then consider taking the warning's advice.
Patches are created by having built two .msi files, and then using the Patch Design view to turn their changes into a .msp file. Certain things, such as dynamic file links, increase the chances that the two .msi files will be subtly incompatible; the "Patch Optimization" setting helps decrease the chance of such incompatibilities by giving InstallShield access to the layout of the previous .msi file. Since InstallShield cannot predict whether you will later build a patch, it warns while building the main .msi file.