Hello Lushoisso56
There is no Bernina Express in Lucerne, PE stands for Panoramic Express. You probably mean, Lucerne Interlaken Express.
If your train ticket is only valid for a certain departure (Supersaver ticket), and Flixbus is late, the ticket is lost, as it is your fault. You can use your ticket for another train if it is a Point-to-point ticket or a Saver Day Pass.
I, personally, would never use Flixbus, too many safety concerns. I would use the train from Milan and in case of a delay, even a Supersaver ticket to Interlaken remains valid for the next departure.
Kind regards,
Roland