I recently went through this exact same scenario with an '06 3.0i. It turned out to be a faulty LCM and ALC. Both had to be replaced. The LCM has to be coded, but the ALC is plug and play.

The timing is suspicious since you didn't have any problems until you removed the lights, but maybe unplugging them and plugging them back in jolted the system enough to damage a module. Who knows? It's kind of nuts that these cars take 6 (six!) modules just to turn on the headlights. Long gone are the days of just a switch and a relay…

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2002 X5 4.6is - Imola Red/Black (Sold)
2001 740i M Sport - Anthrazit Metallic/Black (Sold)
1998 M3/4/5 - Technoviolet/Dove (Sold)
2003 Z4 3.0i Sport - Sterlinggrau Metallic/Black (Sold)
2009 Mini JCW (The Wife's)
2015 i3 REx - Arravani Gray/Tera World (Daily Driver)