cloaking and FLASH

Checking into a big drop in GOOGLE placement under the keyword "Fractions",
I looked into sitechecker.pro and they claim that one of my critical errors is:

Google: page isn’t same.
Cloaking is considered a violation of Google’s Webmaster Guidelines because it
provides users with different results than they expected.

At one time visualfractions.com pages were built with FLASH animation but after
reading that the IPAD and now many browsers are not crazy about running
FLASH aps I decided to switch over to ADOBE ANIMATE CC to write
animations with javascript. All done.
Since then I sent in a new sitemap.xml file that lists only the javascript versions
of the animations. I removed the FLASH versions from the xml file on the site
but the FLASH versions are still on site.

My guess is that is where Google thinks the "cloaking" is going on. I like to leave
the FLASH versions up because there are many links to them.

Here is what I’m considering:
Listing the FLASH animations in the robots.txt files such as:

Disallow: ../CompareL/comparel.html

Any opinions on this matter?