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QQuestion: How can I remove an application function and replace calls to it with something different?

AAnswer: You can also may try this :
In the <compile>in your translation configuration script.  In the <compile> section of the script, do a remove/remove-stubout with a migPattern. This will rework the calls. Then, after the <analyse> <analyse> section, use refactor/remove-delete to remove the original.
Something like this.

Code Block
<Compile Project="%SrcPath%">
<remove identifier="ScanToolLib.readNode" migStatus="stubout" migPattern="%1d.ReadXMLNode(%2d))" />
<Analyse />
<remove identifier="ScanToolLib.readNode" migStatus="delete" />

Since the methods to be refactored were are in a module, it will not be in an IDF (unless you move the module using the SharedFile command) , so these rules will be needed for each VBP that uses the module – unless you moved the module to an IDF using the SharedFile command. 

Another option that is has some appeal is to keep your original application interface calls as is, but to fine tune the implementation to use .NET by hand. Then, use author/replacefile to drop in your fine-tuned file. It really depends on what you were are doing … and if you want to preserve the interface or not.