Both issues sound quite weird. Especially the former one. What Eclipse version are you using? Maybe you have some custom settings to remove various annotations.
For the latter I have a sophisticated guess: the form height is undefined and you are using 100% height customcomponent inside. The Vaadin visual editor creates that kind of components by default so it is easy to make mistake there. The fix is to either define height for the form (and all its parents) or fix the height of the layout. This kind of issues can usually be understood better if developers use the client side debug dialog (opened with ?debug query parameter) and its analyze layouts function.
I have this problem, too!
All @PropertyId will be removed by visual editor by just switching form design and source view.
This is troublesome because I have to add the annotations manually when the design view is used.
Is there any solution to this?