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.

Having those teeth removed will not affect the trays you have now nor will it affect results if you are wearing your aligners 24/7. You may need refinement regardless of whether the teeth are removed or not. I usually find with most of my cases I need some refinement near the end of treatment. I do, however, recommend you having the 3rd molars (wisdom teeth) removed to avoid any future problems.
Best regards!

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.