I fully understand Paypal's need to protect itself from scammers. I get it. The loss potential is huge.
I think the problem here is that they really don't have any kind of a real relationship with their customers.
As an honest business person --not a scammer-- when this kind of thing happens to you it is horribly disruptive and demoralizing. As honest people we should be spending time on our business rather than trying to get our money out of a company that has totalitarian control over it. It could, and has, sink a business.
That said, I feel the OP may have triggered the freeze by clearing the account of nearly all funds a couple of days after the phone interview. If I were looking at that data I would see it as a potential red flag. It would almost be irresponsible not to interpret it that way.
I've had sales in excess of $20K (meaning, the invoice for that particular purchase was $20K) come into one of our Paypal accounts and have never had any issues. Then again, the money tends to stay in the account for months. I don't think they've ever seen us clear large amounts of money out of the account immediately after a large sale. That, I am sure, builds trust, even at the algorithmic level.
> My company empties our PayPal account 2x a month, at which point it's well into 5 digits, and we've been doing this for ~5 years.
Right, but you've been doing that with regularity. It's all about patterns. In addition to that, you are not doing this a day or two after having a probing conversation with a Paypal representative who obviously called with concerns about your account. Huge difference.
I can take almost any amount I want out of our Paypal accounts and it has never triggered so much as a warning email. Our track record (~10 years) is pretty solid.