Wisdom Teeth Extraction During Invisalign Treatment?

At the Invisalign Treatment planning, The wisdom teeth are not covered or not effective at the other tooth movement. Just make sure after removal of the wisdom teeth, the aligners are still fit on the other teeth.

Depending on certain factors, such as age and development, sometimes wisdom teeth, if left alone, can adversely affect ortho treatment; it can cause your newly straightened teeth to mis-align after you have finished treatment. Removing them can be a good idea in that you do not have to worry about any complications they would cause down the road.
The adverse effects mid-treatment would be recovering from the extraction procedure itself; wisdom teeth extractions can sometimes take a little longer to heal, but even then usually within a couple of weeks patients feel okay.
There may be refinements needed and new trays made if teeth have been removed, but it is common to do this with Invisalign; many times as treatment commences changes need to be made and thus new aligners are fabricated.

Refinements would be needed if you were adding to the tooth structure, but since you would be removing tooth structure (in this case, entire teeth), the aligners would not be affected.
Similar to wearing gloves. If you cut off your middle finger, the gloves will still fit. If you grew a new finger, they wouldn't.