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If it's idle, you're okay - the CF slot drains power anyways, but unless the drive's in use (aka: motors are moving), you won't see a significant increase in drain, to judge by the experiences of most of the people who've had one installed. Any drain you do incur during drive-reading or writing can be minimized by having programs using a 'microdrive' mode in which they cache data in a RAM buffer, to avoid having to read from the drive as often.
Also, keep often-accessed or often-modified data on SD card or BIS - the microdrive, ideally, is a read-only drive as far as you're concerned, at least when using it in a PDA application, due to the power drain and the generally slower write times compared to SD or solid-state CF. That SHOULD help you keep your battery usage relatively low, which in turn will keep you watching movies or listening to music longer.
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