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The double-speed poke only worked properly on some 6809 CPU's (I mean down to specific individual chips, not varieties of 6809), others would not return using poke65496,0 due to the CPU crashing (probably because of overheating) and would require reset to recover - on such machines using the double speed poke should be avoided not only because of the crashing but also because repeated overheating could lead to permanent CPU failure - to be honest using it too often even when it works is not really such a good idea.
*The above only applies to "real" Dragons
But look on the bright side - some early Acorn Atoms melted due to CPU overheating when running "normally"

I know from personal experience that some 6809E's can't handle double speed mode, and I do agree that it is possible that some of the one's that can may be damaged at that speed. I have however tested Dragons (and CoCos) by running them continuously for several days at double (POKE65497,0) speed with no apparent ill effects whatsoever. IMO, If you have a decent Dragon it won't be harmed by the double speed poke. If your Dragon does run OK at double speed, and you are worried about the 6809E being damaged, replace it with a Hitachi HD68B09E, HD63B09E or HD63C09E. Brand new HD68B09E's can currently be picked-up for less than five pounds via eBay.