You have to do "make dep" any time you change your configuration, or any time you "make clean." Same goes for "make mrproper." BTW: what I do is to copy my .config to another place outside the kernel source tree once I get a stable kernel. Then, when I want to build a new kernel, I put the .config back, do a "make oldconfig," and the rest of the steps. It makes life easier both for upgrades and recompiles of an existing version. I back up .config again each time I upgrade or change something, of course.
