Flash alternatives...

Canvas animations, javascript, jquery are just a few examples that can replace what your client is currently doing with Flash.
You'll need to pick the tool that matches the complexity however, some really complex Flash files that use 3D models for instance is not something that i have seen the canvas implement yet, though in saying that they managed to get an entire game running in the canvas.

 

There's the SmokeScreen library. It's still in development, but has the easiest interface.

JavaScript is really the only option, unless some of it is simple enough to do with CSS. Nothing else really provides client-side animation capabilities. jQuery has a lot of nice plug-ins that can give you various effects more easily than creating your own.

 

I feel your pain... my studio is seeing a bit of this too. Currently you have two options: javascript or a custom app for the ipad in objective C... so for your purposes javascript is probably the way to go.

*someday* the best replacement for Flash may be... Flash!

Currently, you can copy animation off the timeline as XML, and last year Adobe showed demos of "smart pasting" this code into a canvas tag using Dreamweaver... so, the ability for Flash to output either to SWF or HTML5 is probably not that far away... Flash CS5 is ready for this, it seems that dreamweaver is not.

in the meantime, if you do have a lot of assets currently in flash format you need to repurpose, the FLA as XML structure (CS5 only) can come in quite handy... simply change .fla to .zip and you can open the file to have access to all of the image assets, motion XML, type settings, code etc.

AS3 and javascript are very closely related, so you can repurpose some of the logic as well.

But aside from having all the assets in hand, you are officially "off interface" and will need to use javascript to rebuild all the work from scratch. Charge accordingly!

 

FlashCS5 outputs a pretty good HTML container for Flash using swfobject.
You can include the Flash data in the alternate content div, using PHP.
(assuming here that your SWF is loading data from an external source such as HTML, XML or PHP; if it's not, it should be)

You can then format this data for the iPad (and other crippled devices) with whatever technology you want; AJAX, HTML/CSS, HTML5 etc... while retaining the existing Flash content for desktop web browsers.
My favorite method right now is to use the Dreamweaver Spry framework, since it is so simple to setup, and the results are a lot nicer than basic HTML/CSS.