Owners of previous versions should uninstall the old version before installing version 4.0. The Help File can be left as is (assuming you are going to put version 4.0 in the same place). Remove all packages from Delphi and close all projects in Delphi. Only then, should you build the IECS version 4.0.
Version 4.0 represents quite a few changes in the engine "underneath" to make it compatible with Vcl and FMX. As much as possible, source code compatibility was kept, but some changes were unavoidable.
The major change in the IECS v4.0 is the addition of modules.
Some object pascal functions were moved (specifically from IEHelperFunctions to HelperFunctions, IEVclHelperFunctions and FMX.RS.IEHelperFunctions).
Vcl-specific IECS functions (such as show-message and input-query) were moved from their TXXXPackage to the new TIEVclPackage. You need to drop a TIEVclPackage onto your form and hook it up to the TInferenceEngine to recover those functions. For new FMX applications, you would drop a TIEFMXPackage onto your form to have access to those functions (i.e. show-message and input-query).
Most components can work with either Vcl or FMX, including the TInferenceEngine, TMathPackage, etc. However, the TConsoleDialog, TRulesDialog, etc are Vcl ONLY. Their FMX equivalents are named TFMXConsoleDialog, TFMXRulesDialog, etc.