Here is an example of the join filters that I am referring to that DO work.
Celigo Magento 2 Customer Id Map Netsuite record type, created by the Celigo Netsuite bundle.
In an integrator.io Import step, selecting this record type, selecting “Add or update”, then viewing the lookup criteria:
The available filters list contains join fields for all fo the “List/Record” relationship fields on the Netsuite record type.
But for many of the custom record types that I have created, these join fields don’t show up in the lookup criteria. Only the record type fields show. Why? How can I get the join fields to show?
I have refreshed the metadata for the Netsuite connection. I have refreshed the search filters in the popup. The record types that are missing the join filters do have an at least 1 entry that can return in a search. The record types have the same configuration and permissions as the record types that were created by the Celigo Netsuite bundle.
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Will check with QA. In the meantime, you could use formula(numeric) and then use a formula like {custrecord_celigo_field_id} and the set the value to equal your record field.
I assume you think I am adding a search filter for an Export using a Netsuite saved search?
I am actually attempting to add a search filter on a Import to Netsuite, using “add or update”. The search filter is to identify if already exists. If I could specify the join-filter manually, I would. 
Oh, wow. My apologies! I missed that option, even though it was in my screenshot. 
Thank you!
Hmm, interesting. I do see the Formula options on production, but NOT on sandbox.
The record types are identically setup on Netsuite, I cleared the connection metadata and refreshed the search filters.
Does your sandbox account have the latest Celigo SuiteApp version installed? We aren't able to push updates to sandbox accounts so it may be outdated.
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Ah, the bundle on our Netsuite sandbox is indeed outdated. I will update it and assume that is the fix.
Thanks again, @tylerlamparter !