Got the same issue here. On 1.12, engine sounds seem to stop working sometimes on a time warp. It might be related to mods we are both running but your mega.nz download link to the text file with your mods stopped working. I had all the same mods installed on 1.11 and never had this issue. Some of them I've updated, some of them I've yet to.
Running MechJeb2 2.12.1.0, SCANsat 20.4, StageRecovery 1.9.2.2, TimeControl 2.10.0, TweakScale 2.4.5.1, All Y'all 0.11.19, Easy Vessel Switch 2.1, Scatterer 0.0632, and KSP Recall 0.2.0.4