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.
New Project....... 2.4L Long Rod motor for my EVO
03 Evo 8 HTA3582r Blown Motor
09 e92 335i MT Sold 440hp/480tq