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The filter in your IsoConfig.xml is probably not set up to allow for it. The default filter definition is:
<Filter Name="FLValve" Value="Type LIKE 'VALVE*' AND (End1='FL' OR End2='FL')" />
What is your end type set to on your lined flanged valve?
By default, 2" and below uses the small bore theme. You can either change the limit for small bore to be smaller, or switch to the small bore theme in the iso config UI in project setup and enable string dimensions.