I have no idea whether this has anything to do with the recent problems with downloading, duplicate securities, etc. But shortly before the long outage last month (during which I had no problems even though my wife did) I had a securities mismatch for my Vanguard institutional (no ticker) funds. I went back into my register, sorted by security and basically renamed everything to the "new" security information that I had downloaded. It probably took me about 30 minutes -just a minor annoyance in the scheme of things.
For my S&P 500 fund, the first time this happened, I simply added a "b" to the name I was using (the downloaded name was VANG INST 500 IDX TR), to match the new downloaded security information. I deleted the old security, which I had earlier named VANGUARD INSTITUTIONAL 500 INDEX TRUST.
This worked fine for about a month, and then this morning, the issue arose again. The same thing happened with the security I had named VANGUARD RETIREMENT SAVINGS TRUST II, although in this case I didn't delete the security and you can see it in the dialog below (the "b" is just something I did to differentiate and match the downloaded information). I am not aware of any changes to the underlying securities. I guess I'll go back and do what I did earlier, but this is now getting super annoying.