You can change the email alert option settings on the BPS Pro > Display & Alert Options page > Email Alerting & Log File Options
When installing BPS Pro after manually deleting the BPS Pro plugin folder you can prevent these email alerts altogether by going to the WordPress Plugins page and clicking the Must-Use link at the top of the Plugins page. If AutoRestore is turned Off you will see – “AutoRestore is turned Off” in green font under the BPS Pro MU Tools must-use plugin. If AutoRestore is not turned Off then click the “Turn Off AutoRestore” link.
After AutoRestore is turned Off you would then activate BPS Pro on the WordPress Plugins page.
Then run the Pre-Installation Wizard and Setup Wizard.