This is something that annoyed me as well. I found a way to get rid of the warning. While this might potentially have some negative side effects, I did not experience any, so give it a try:
In Innovator/Client/javascript/search_container.js change line 584ff (for 12SP8 at least):
from
[embed:dc8ab71f-3b98-42d9-b0f6-e21e02a0f8e2:e424bf51-6f83-4e29-9973-58d42cdd62b9:type=csharp&text=const%20bSwitchToNewSearchMode%20%3D%20aras.confirm%28]
to
[embed:dc8ab71f-3b98-42d9-b0f6-e21e02a0f8e2:02dadca1-e47f-4c90-8c37-4502636061aa:type=csharp&text=const%20bSwitchToNewSearchMode%20%3D%20true%3B]
and remove / comment the subsequent aras.confirm() statement completely. This removes the warning (which is not needed at all in my opinion).
\Ralf
