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When exporting these MARC fields based on the MARC tag, you must specify all subfields in the MARC field when exporting this MARC field. Let's take the following example: I want to retain call numbers from my bib record 090, 050 and 086 MARC fields. In some cases, there may be call numbers in item records that I want to take precedence over the above bib record call number fields. These are correspondingly the item record 090, 050 and 086 call number fields. The following image shows what each MARC FIELD export would look like. Note the inclusion of the subfields in the field export:
For the 6 fields listed above, this is what my complete list of call number fields would look like, right before I export them from Create Lists:
This is what my file looks like when I open it in Notepad. Note that you should see semicolons (;) in between the call number subfields. This is what Ex Libris uses to migrate the call number fields to the separate $h and $i fields in the holdings record.
Note that in my file there are now column headings that are identical (I have two 050|ab headers, two 090|ab headers and two 086|abcd headers). Because of this, I must alter my items file so that these duplicate headers don't exist in the file. If you are only exporting call numbers from either the bib record or the item record, you can skip this step. This step only applies if you are exporting the same fields from both the item record and the bib record.
The column headers can be manually modified, but you can't do this modification in Excel, as doing so can impact the integrity of your data. Open your item file in Notepad or a similar text editor in order to change the headers in your items file so that every column is unique. This is what my modified items file looks like now. I only need to change the last three columns in order to make every column header in my file unique. 
The column headers that you modify can be whatever you like. However, they must match whatever you place onto your Field Mapping form under the Items tab call number section.
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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.
This is what a successfully migrated call number looks like in Alma after taking this approach.
