If you are removing a class you can do that through the DBC script associated with the product.xml, something like the following, which will remove the class from the INVUSELINE .ISSUETO when you run the updatedb.bat / sh.
I did not test this specific script so you may need to adjust it.
<?xml version="1.0" encoding="UTF-8"?>
<script author="Alexey Potanin" scriptname="V1000_01">
<description>Add Barcode Printing configurations.</description>
<attrdef attribute="ISSUETO" classname="" />
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Blatant self-promotion, but if you are interested in using the product.xml and DBC scripts to manage your configurations, you might want to check out the blog I wrote on migrating screen changes with the mxdiff utility.
The resulting mxs files can be used in the just like DBC scripts, which is pretty cool.
A project that uses this can be found here.