Notes 9.3 (iPad Air) only saves first page of PDF

Consider yourself lucky that your iPad Air is not a brick.

If I were you, I would Contact Apple Support - AND - file a "bug report" from the menu choice on this form > http://www.apple.com/feedback/ipad.html

In case you are unaware, take look at the common topics in the appropriate forum > Using iPad

Rosefool wrote:

Thank you for your suggestions.

RE: iPad Air as brick...are you saying I need a new iPad?

You're welcome.

No. Not unless you were thinking of getting a new one anyway 😉

Apple rolled out a very buggy iOS 9.3 - newer devices just MAY experience "weird" things - older ones are "bricked" = read on, but I fear that your issue is not among these

The "list" of pertinent articles as I know them to be as of now

- you can read about the problems in these articles, and possibly find workarounds, particularly in the last one

• If you can't activate your iPhone, iPad, or iPod touch after installing a software update - Apple Support
• Apple pausing iOS 9.3 updates for older devices, working on activation fix | iMore
• Apple releases new build of iOS 9.3 for users of iPad 2 affected by bricking bug | 9to5Mac
• Apple Addresses GSM iPad 2 Activation Bug With Revised iOS 9.3, but Broader Issue Remains Unfixed - Mac Rumors
• If you can’t activate your iPad 2 (GSM model) after you update to iOS 9.3 - Apple Support
• Troubleshooting iOS 9.3 Update Problems