You can use this solution : http://www.jonathanantoine.com/2012/08/06/keep-access-to-filesfolders-the-user-granted-you/
Store it in the FutureAccessList:
var picker = new FolderPicker();
picker.FileTypeFilter.Add("*");
var folder = await picker.PickSingleFolderAsync();
StorageApplicationPermissions.FutureAccessList.AddOrReplace(Token, folder);
And get it back :
var folder = await StorageApplicationPermissions
.FutureAccessList.GetFolderAsync(Token);