Ok, the next way to do it would be with Windows API calls. There are API calls GetFileVersion (or GetFileVersionInfo).
However, there's no SetFileVersion API call. Well, at least I didn't find anything like that.
Finally I found StampVer, a freeware utility to change version resource of a Win32 executable (there may be other similar tools). Since it seems quite impossible to use VB.NET directly, could it be possible to use a third-party tool. Now you could call the utility with Shell or use System.Diagnostics.Process class.
For Each ctrl As Control In Me.Controls("pnlMainPanel").Controls
If ctrl.GetType Is GetType(System.Windows.Forms.Panel) Then
For Each subCtrl As Control In ctrl.Controls
If subCtrl.GetType Is GetType(System.Windows.Forms.TextBox) Then
If subCtrl.GetType Is ...