How do I upgrade APPX 3.5 or 4.0 to version 4.1?

The following should get you from Appx {3.5 or 4.0} to {4.1 or 4.2} pretty directly:

Confirm that your "MNT" (maintenance) registration cutoff date on your 2nd registration screen has not expired.
Download Appx 4.1 from our www.appx.com > Downloads > APPX Server Releases.
Run setup.exe (Windows) or install.sh (Unix), overlaying 4.1 on top of 4.0.

You must be logged in as Administrator in Windows, and as root under Unix.

Delete all EM and Dbg directories ($APPXPATH/*/*/EM and $APPXPATH/*/*/Dbg) for all of your Design Files and the Appx 0-App files.
Scratch all '$APPXPATH/*/Tmpdata' directories.
Create system files new to 4.1: Run System Administration > System Setup > System Administration File Management > Create Files.
Go to System Administration > Database/Applications > Applications.

Go down the list of your Applications.

For each, perform 'Design File Management' > "Convert From Pre 4.1 to 4.1".

Do *not* do this for the four "0-apps".

Optionally run "Create Executable Modules" while on the Design File Management screen.
For users using the GUI Appx/Client, download and install the current 4.1 Appx Java Client onto their PCs.

For users using the Win32(Windows) Client, download and install the current appx.exe client onto their PCs.

10) Once 4.1 is operational, update its Structure files to prevent future export/import problems:

10a) Delete each Application's APPXPATH\vv\aaa\Struct directories and their contents, where aaa\vv is your ApplicationID/Version#.

Do not delete your four 0-app APPXPATH\00\0*\Struct directories.

10b) Run System Administration > Database/Applications > Applications > Design File Management > Create Files, for each Application/Version pair, to recreate its Structure files.