Jake,
Personally, I am convinced that Flash is not the optimal technology to build websites, and I am not the only one have this opinion, but as you point out that's besides the question.
However, if you want to use Flash, you'll have to do it properly, both for SEO and for your users. This is not a question of following the sheep, or some biased opinion of a bunch of flash haters, it is a fact.
For your users: each time have opened the site - it took an extremely long time to load - and I ended op with a page showing only the navigation in the middle. This can also be seen on the load video I inserted from Webpagetest that you can check here.
For SEO:
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Flash can be indexed (https://support.google.com/webmasters/answer/72746?hl=en#1) - however you block robots to index any .sw* file.
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You serve different content to robots & human users - that's called literally the definition of cloaking, and is considered a violation of Google Webmaster Guidelines. See https://support.google.com/webmasters/answer/66355?hl=en : "Cloaking refers to the practice of presenting different content or URL's to human users and search engines". The url's indexed in Google are static HTML pages which in normal conditions are never seen by your visitors and they are different from the url's you serve to human users.
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as mentioned in my previous remark - you also block the indexing of .js files - where google clearly states that this can have an impact of your rankings.
If you would hate that somebody would think "Flash is bad" based on this post, I consider it a scary thought if future readers of this post would think that it's ok to completely ignore the Google Webmaster Guidelines just because you seem to get away with it (until now).
If you are convinced that this drop is caused by negative SEO, you are free to do so. Maybe there is a correlation between the sudden drop & the events you describe. The truth is out there...
But, there is plenty that you can do on your own site to improve your ranking and defend yourself against the effect of any negative SEO attempt.
rgds,
Dirk