It will definitely affect the autodetected baseline and you will need time to train again the autodetection of your baseline. A best practice is to leave the autobaseline as it is and create Custom alerts for your SLAs metrics.
With this approach you will be able to get alert on the conditions you want and still get information of the current behavior or your service (and together with the AI will alert you when something is abnormal)
Thanks for the answer Rodrigue, this is what I think as well, so now I can reply customer confidently.
Another question though: I did try custom alert, but seems like not able to utilize tags to filter the scope of the custom alert. Do you also face the issue of not able to utilize tagging as filter in creating custom alert?