Summary:
Change the delta sync logic for invoice_item, credit_memo_item, and debit_memo_item tables to not only use the updated_date of these tables, but also the updated_date of the related parent documents (invoice, credit_memo, debit_memo). This will ensure that the home_currency fields will be filled with the correct values if any invoice, credit_memo, or debit_memo changes its status from Draft to Posted.

Background:
Zuora documentation about Foreign Currency Exports:
https://knowledgecenter.zuora.com/Zuora_Collect/Zuora_Finance/D_Finance_Settings/F_Foreign_Currency_Conversion/Foreign_Currency_Conversion_for_Data_Source_Exports

It sais:
You can export currency conversion data for the following data source objects:
Invoice - Currency conversion data is provided for posted invoices only.
Invoice Item - Currency conversion data is provided for items in posted invoices only.

That means if the Invoice changes its status from Draft to Posted, we also have a change in the Invoice Item object itself: The field charge_amount_home_currency of the Invoice Item object changes its value from NULL to the actual home currency value. However, Zuora will only update the UpdatedDate value of the Invoice (because the Status field changed it's value from Draft to Posted), but will not update the UpdatedDate value of the InvoiceItem.

The result with the current implementation is that Fivetran will not capture the update in the invoice_item table and the charge_amount_home_currency value is NULL which is incorrect and not in sync with the value in Zuora. A full resync would proof this.

We've received an official answer from Zuora how the delta sync strategy should be adjusted to not miss any updated records (quoting Zuora Support's answer):

"I reviewed the info you provided and as I explained before, FX rate is only used for reporting, and when reporting generated, system will grab the FX rate, and calculate the amount in home currency, in real time to generate the report. So here, if I understand your sync process correctly, Fivetran is using updated date to grab the delta load and since the invoice item updated date has not been changed, this item could not be grabbed by Fivetran. However, as the invoice updated date has been changed, is it possible to use invoice updated date as a filter to export the invoice item you need? 
[...] 
For credit memo and credit memo item, it is the same as invoice and invoice item, when the credit memo has been posted, the credit memo updated date will be changed, but not for credit memo item. 
 
I am not fully understand how Fivetran sync works, however, to extract the data from Zuora, please try if you can use invoice updated date as a filter to export invoice item data you need."

PS: I highly consider this not a feature request but a bug which should be fixed ASAP. Unfortunately, Fivetran Support insisted that this needs to go through this Feature Request process... :-(