...
If you do wish to include the CALL#(ITEM) field, you may do so, but turn off the setting under Settings | Create Lists | "Look up call numbers". Leaving this setting on will cause the CALL #(ITEM) field to be fully populated, and will subsequently override all other call number fields with a call number that does not contain the $h and $i subfields. If it is important to retain the $i in the holdings call number, I would suggest not exporting the CALL #(ITEM) field from Sierra/Millennium at all.
This is what my Field Mapping form looks like for the situation outlined above. Note that I am not including the CALL #(ITEM) field at all. My modified headings '090|abitem', '050|abitem' and '086|abcditem' are listed before the bib record call number MARC fields, because I want the item call number fields to take precedence. If you wish for the bib record call number fields to take precedence, you would list the corresponding MARC fields for the bib record call numbers first.
...