Hey op. Did u try erasing all & any previous codes prior to setup? I too have a 11' 35d. And just got through a roller coaster with my homelink. I have an older genie and used a Chamberlain universal and no luck. I bought online the older Genie remote and all worked in as should. The Chamberlain universal remote did not have the homelink available feature. But I read up on homelink site that some remote itself needs to be pressed/ set into program mode then simultaneously pressing the desired homelink button. And go from there.
Good luck.

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2011 X5 35d 123,000 miles sport space gray/oyster

2005 X5 3.0i sport package Style 211
157,500 miles

2005 Chevy Avalanche Z66 BFG T/A Offroads