I think Sidious always had it set up for the CIS to lose. The whole war was orchestrated from the start in such a way that whatever happened, Palpatine would end up on top and the Jedi would be wiped out.
Instead of Emperor Palpatine with his Moffs and Stormtrooper legions enforcing the New Order, there would instead be Emperor Sidious with his Corporate Governors and Droid legions enforcing the New Order.
Then at the end of the war, the 'Separatist Council' would have gone about establishing their new government to rule over the Galaxy they had just conquered - and since the Separatist Leaders all answered to Darth Sidious, it's a pretty safe bet that Sidious would have things set in motion so that he would be installed as supreme ruler of that new government. With the Jedi fighting on the front lines, if the CIS won the war then they would have wiped out the Jedi in the process, so there would be no need to enact Order 66 (although Palpatine still might have done so, just to be sure there weren't any Jedi survivors). Would order 66 still happen idk very confused what would happen
