My take as a former white-collar investigator: Manafort recently produced a variety of documents in response to voluntary document requests. The total number of documents he produced was quite small. He also produced documents to and testified before the Senate Intelligence Committee shortly before this raid.
The investigators (either at Senate Intel, the FBI, Mueller, or possible all three) likely knew of the existence of certain documents prior to making those requests through intelligence or the treasury or otherwise.
I suspect that when Manafort's production and testimony failed to include key documents investigators already knew existed that gave them probable cause to suspect he was hiding those documents (or as the poster above suggested, may destroy those documents), and possibly others. At least, that is usually what is going on behind the scenes when you follow up voluntary requests with a search warrant.
We know that Manafort turned over documents to the Senate Intelligence Committee in late May 2017. We also know that the Senate Committee sent a request relating to Manafort's finances to the treasury in early May 2017. According to WaPo/NYT reporting, this search warrant was executed in late July. Manafort met with investigators for the Senate Intelligence Committee on July 25. According to this article, the raid took place the following day, on the morning of July 26. Manafort also produced documents to the Senate Judiciary Committee on August 2, 2017, but that appears to have been after this raid.
I believe this quote from the article supports my theory:
Investigators may have argued to a federal judge they had reason to believe Manafort could not be trusted to turn over all records.
as well as these quotes from the related NYT article out a few minutes ago:
NYT reports that Mueller investigators searched Manafort's home for "tax documents and foreign banking records."
The F.B.I. typically seeks such records when investigating violations of the federal Bank Secrecy Act.
The search was carried out shortly after Mr. Manafort met with investigators for the Senate Intelligence Committee on July 25.
Since this post is visible, I would also like to add this interesting take retweeted by Chris Hayes at MSNBC. The anonymous sources for the WaPo article appear to be defense-side, while the sources for the NYT reporting appear to be from the side of the investigation.
Finally, to clarify my experience, I am a lawyer who worked for the banks on internal white collar investigations (and defended them in white collar investigations) I am not former law enforcement.