All good reason to keep working on it.

The questions you ask are very complex. The short answers (and then I'm really leaving the question at that point until a longer article is ready):

• Rehydration involves pulling off the stabilizer molecules (glycerol, trehalose) and replacing them dynamically with water. This can induce folding changes, some of which are irreversible. This is not theoretical: many biochemists have to deal with this in their daily work.
• Membrane distortions also distort relative position of proteins within that membrane (and the structure of synaptic scaffold, a complex protein structure that underlies the synaptic membrane). Regenerating the membrane and returning it to the original shape and position doesn't necessarily return membrane-bound molecules to their original position.