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Because my Beamer files are large, I split then into separate .tex files and start a new part with e.g. 

\addtocounter{section}{3}

This works in that the first section in this .tex file correctly appears as Section 4 (correct also in footlines and headers).

However, in the TOC on the first page of the PDF, the first section appears as section 1, not as section 4! Same with the sections that follow: they appear as 2 and 3 in TOC, not as 5 and 6.

Is there a separate counter for the TOC? If so, how can I manipulte it?

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Write the following somewhere in your preamble: 

\makeatletter
\advance\beamer@tocsectionnumber by 3
\makeatother

This might have other undesired results but this steps the number in toc. Note: beamer does many things different form latex2e, this is one example. If you are interested in further investigations on this take a look into a "normal" toc file an beamer's toc file.

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It works, thanks. No undesired side effects so far! – Keith Dec 10 '12 at 6:21

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