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Creí haberlo añadido en el tag del quote, siempre lo hago. Es YahooAnswers.
De todas formas cito otra opinión más fiable, desde Technet.
This file only gets created when you run some software that requires to chkdsk (Disk Check) when computer is rebooted, after the task is complete and the operating system is running, you can safely delete this file.
It doesn't replicate after deletion because it is no longer needed, it will only appear again when you will run another Disk Check at system reboot.
AFAIK presence of bootsqm.dat indicates that the disk was checked (chkdsk) and this probably "fixed" some errors on the disk. I guess during this process access to your data was somehow lost.
Zorronde, puedes eliminar el archivo sin preocupaciones, aunque deberías realizar un análisis del estado del disco, por prevención.
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