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Nope.
The kitchen makes a ROM image (Read Only)... just like you can't erase something off of a CD-R after you burn it.
However, the conflict you're talking about has probably resulted from the fact that the cab file has installed the application to its normal location, whereas when you build an application into the ROM all of its "stuff" is located in \Windows. If you're experienced enough you possibly could move all of the newer files to \Windows using Total Commander. The OS will allow newer files to "overwrite" files in ROM, however they're not really overwriting--just hiding the originals.
Keep in mind it still may not work properly if there are entries in the registry referencing the normal install path (like \Program Files\App rather than \Windows).
It is one of the downsides to using the kitchen. If there is an app that is updated frequently my suggestion is to not build that app into the kitchen. That way you can easily update it later without having to rebuild the ROM.
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