Yoast Plugin Permalink problem

Few days ago I have changed a setting in the yoast plugin under advanced section. I have under advanced in the permalink section change the category settings. I change the pointer from keep to remove and right after 3 to 5 days all my keywords that are ranked in Google are gone. And now they are not even in top 100.
And then I have selected the pointer back to keep and almost 4 days have been passed and nothing happened.
Can you please tell me will it fix the problem automatically or I have to do something else.


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