If I disempower a Kayle, Justified who has been empowered 3 times, does she lose all of her empowered statuses?

No. She will lose one of her empowered statuses.

For every Riftbound card other than Kayle, empowered is a binary status. They are either empowered or not. Kayle utilizes the golden rule “Card text supersedes rules text” to overcome this and be able to escape the normal bounds of what the empowered status means. On Kayle, empowered isn’t a binary status but a stacking status; she can have up to 3 empowered statuses. When Kayle is disempowered, the disempower action attempts to remove the empowered status. If she only has one empowered status, great, it’s gone. If she has more than one empowered status, the disempower action will remove one of the empowered statuses from Kayle.