3/8th of an inch of filler is to much...that's one of the reasons that the filler is cracking. I can't see the previous repairs in the pictures so it's hard for me to give you concrete advice but, chances are you would be better off to replace the previous repair with new metal. If the filler is cracking it's because it was put on to thick (1/4 of an inch, which is what most filler manufacturer's recommend to be the maximum depth or amount of filler, is more than what I would ever put on on one spot, let alone 3/8 of an inch and when you dig the filler out, chances are you find rust underneath it). When filler cracks, water gets in the cracks and filler is a sponge and will suck up moisture causing the metal underneath to rot.
Yes, with out a doubt, you are doing the right thing taking the car down to bare metal.