It actually makes sense when you think about it. The "tough" ballots -- where the intent of the voter may be clear, but which tend to screw up machines (partially filled-in ovals, for example, or something else depending on the technology used in your state) are generally the fault of less educated, downscale, low-information voters. Who do those folks tend to vote for? Democrats. So it makes sense that in recounts, the Dems will generally pick up votes from rejected, challenged or provisional ballots.
Not to suggest there isn't ALSO hanky-panky going on, just saying that the law of averages is misleading if voter bases are different.
The increase in the lead is apparently mostly due to officials uncovering undervotes in heavily Democratic areas like Fairfax County, which use paper ballots. In a somewhat ironic twist, most of the redder jurisdictions in Virginia rely on electronic voting machines that leave no paper trail for individual votes, so there simply weren’t undervotes to be discovered there.