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Is there a way to update the subsidiary in before submit? I tried but getting unexpected error.
Otherwise, is there a way to update primary subsidiary of the customer?

It would be likely due to sourcing issues. Not sure if it would work but maybe try beforeLoad?

Changing the subsidiary beforeSubmit is not a good idea. All the other fields are sourced on the subsidiary (currency, departments, locations, items, etc.), so when you change it, lots of fields are cleared or reset.

Can we change Primary Subsidiary of the customer?

Yes, in the UI you can use the checkbox to mark the primary sub, but on SuiteScript I'm not sure how to do it.

Yep, there is a subsidiaries tab in the bottom.

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I don't see this "Primary" checkbox under Subsidiaries sublist on the customer record. <@U03A2UBF6BE>

I think this checkbox is only shown until no transaction is posted for that entity.