It also makes sense that it’s crashing, because @andrei reported the duplicates were at the bottom of his sheet, and so it crashed before reaching auto-sort after fill.
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In my testing, Auto-Fill now runs during the 12am, 6am, 12pm, 6pm hours, independent of what time I toggle Auto-Fill on.
I personally like the 6am fill to focus my time-driven scripts around and it’s also closer to when the Hello Money email comes out, so that email is more in sync with the data in my sheet while I’m sipping my morning coffee and checking status 
So far, I haven’t noticed a case where Fill kicks off while I’m interactively doing something in the spreadsheet. More frequent fills hopefully means faster fills, although I don’t get enough daily transactions (handful at most) and don’t have very many total transactions (~5300) to be a very good stress test 
I checked on my side and Date Added looks good (both Transactions and Balance History sheets). As you said, it’s unchanged, plus I confirmed that the Date Added date-time is the local time from the spreadsheet’s settings, and not UTC 
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Note an update I just shared here about these changes:
A post was split to a new topic: Amount polarity question