What errors can I expect by changing DOCTYPE from XHTML strict to Transitional?

Hi there,
I have recently built templates for quite a large content-managed website in XHTML strict. Unfortunately, I didn’t foresee the back-end development(I’m told it’s ASP.NET) to be churning out code that doesn’t validate as strict DTD .
I have changed the doctype to XHTML Transitional in my static html templates, and so far I don’t see any display problems, however I am worried that I may be overlooking something important/obvious, which could cause major problems with the site at this late stage.
There are flash and javascript applications on the site (as far as i’m aware).
So my question is:
Could changing the doctype from Strict XHTML to Transitional break *anything* on a site – client- or even server-side -wise?

Thanks

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