I highly doubt any tune will cause permanent hardware damage. I've seen too many times shops don't know what the cause is so they blame the "software". Exactly what is wrong with your car? What year? There have been a few DME failures lately, it is starting to look like the new HPFP for those build dates.
2011 335is DCT, JB4 MHD BEF, stage 2 LPFP, e50 50/50 meth, FBO, MT ET Streets when needed