It`s completely safe. Funny enough I had the same worries when I first did it.
Most people dont know this but when you reconnect it, go in to the car and PUSH UPWARDS on the sun roof electric switch (not back and not forwards, just up) and HOLD it for about 1 minute until the roof gives a quick movement. I dont know exactly what this does but I know it`s BMW`s official priming routine after a battery disconnection.

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X5 3.0D 2003
Mods:
Webasto telestart remote kit
Aluminium running boards
Tv in motion & Aux input lead, Ice>ink to Ipod 3g.
DVD rear headrest screens and dvd sytem integrated in to main tv system via aux lead (watch tv or dvd in front and back)
Homelink Gate Opener, Chrome Grille Kit, chrome tailgate handle, Chrome Guage Rings, Tunit V-CR 086
Standard:
Bluetooth, comms pack, sat nav, sports pack, sports seats, dimming mirror, electric folding mirrors, memory seats, heated seats.