Ungroup objects don´t remember layers

Jana,

In addition to what Ton said, referring to this, "After the newest update of illustrator and indesign I found one problem", are you sure it was different earlier?

What happens/happened to the object from different Layers at the moment you Group them (other than their jumping into the topmost Layer)?

If applicable/viable for your purposes, you may consider this Select option:

1) Select the objects across Layers, then in the Select dropdown Click Save Selection and give it a name;

Affter this you can still do things to the individual objects within their respective Layers, and you can also:

2) Click the name given in 1) and do things to the selection, hopefully the things you wish/need to do.

Illustrator does not have an option to restore layers after ungrouping.