Delete the current phars of the plugins you have and replace them with the updated versions. This would require that the developer(s) of said plugin (or another developer contributing to it) has made an updated version though.
That's terrible advice: you can easily corrupt your worlds and plugin data. Many plugins are already updated on Poggit for API 3.0.0, and to update your own plugins you should check the Changelog for recent PocketMine releases to see what needs changing. For other plugins the wisest approach is to ask the developer to update as Edwardthedog2 suggested.