How can I match text only at the end of a file?

There is no way to write a rule which is “match this text, but only if it comes at the end of the file”. You can fake it, though, if you happen to have a character lying around that you don’t allow in your input. Then you redefine YY_INPUT to call your own routine which, if it sees an ‘EOF’, returns the magic character first (and remembers to return a real EOF next time it’s called). Then you could write:

<COMMENT>(.|\n)*{EOF_CHAR}    /* saw comment at EOF */

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