After following the instruction below, Quicken asks to either create new account, or link to an existing account. However, I have several Vanguard accounts (Roth, Trad IRA, Brokerage, etc) so it is unclear which to select. In past I have downloaded each individually and imported them into Quicken, but that takes a lot of time. Any help doing a single download of all accounts at once appreciated.
Pete
Sorry, I can't offer any advice. But I feel compelled to share that I have no desire to risk screwing up my account history by taking this approach. I did that once, and removing the resulting duplicate entries was a major waste of time.
If you get a message about linking a Quicken account or creating a new one, cancel the import and for each account you are trying to update, click on the gear at the top right and then Edit account details. Compare the account numbers shown there to the numbers in Vanguard's list and correct the numbers in Quicken if necessary.
If you have been downloading the Vanguard account for many years, Quicken may have an account number left over from the old mutual fund only system or Vanguard's old Pershing brokerage platform. For more info see Page 11 of the main discussion about the Vanguard outage here.
I am going to wait until they solve the problem and the downloads work automatically again. I too have several Vanguard accounts and was confused by the language in their instructions. Without taking the time to find them exactly, IIRC it said if you want to get all your "funds" in a single file click here, if you want to download your funds separately click here. What, I wondered, does "fund" mean in this context? Account? Individual holdings (i.e. individual vanguard (mutual) funds? I spoke with three separate Vanguard tech support agents and none of them could define the term in that context. As 
gpsabol
said, cleaning duplicates is a waste of time. I could try it and if it doesn't work go back to the pre-import version of my Quicken data file via Time Machine (I"m on a Mac) but it's not that pressing. Frankly, the way the markets have been the past few days, I am probably better off not knowing.
I think Vang met accounts instead of funds
I download accounts individually and import them individually to Quicken. Found that works.
If Vanguard can solve this issue in a timely way, perhaps I should consider moving all my funds to another company, thinking Fidelity.
The accounts versus funds depends on which VG platform you are using. If using their old “mutual fund only” platform, each fund is its own account and should be downloaded by itself. If using their brokerage platform, which supports ETFs and mutual funds, you download each account (eg., your IRA, spouse’s IRA, taxable).
Makes sense, but why couldn't any of the three Vanguard reps I spoke with (escalating to supervisor and specialist levels) answer? Offshoring customer service to people for whom english is a second language (at best) and forcing them to rely on scripts is a real problem
my transactions just downloaded!
