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If the column layouts are defined on your derived templates, then they will not be affected - only the column layouts of the actual "system" templates (Text, Document, Search [template], will be affected.
If you have customized the "system" template column layouts, I would recommend that you copy your .urd file, do a Full Repair on the original, and then manually update the few "system" template column layouts to match the copy... I would suspect that this will be unnecessary since you have likely done your customizations to non-system templates/items, but if it does, you can simply revert to the copy.
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