PS-3 only go through the morse code beeps or Led flashing when it recognizes a different flash code being loaded. It then compares the two. This happens on a power cycle. So if you load a new chain file, and turn power off it does the comparison. But it runs out of super cap power. When you reapply power it finishes the comparison and then loads the new chain file. You need to let this happen. When it is done it starts up.
When a PS-3 board starts up it looks not only at the hardware table, but at the Sound file characteristics especially for lighting. MTH made a change in software to account for using PS-2 3V SF in PS-3 and PS-32 boards to get this info from the Sound File vice the hardware table. So that you get the correct attributes for the PS-32 boards.
So even though the chain file becomes new, it started up on the old chain file looking at the sound file. If you now directly load a new sound file, those attributes will not be used until the next power cycle. Since the chain file is changed, no more morse code, it just uses the new sound file data. If you change the flash code and then sound file without a power cycle, on the next cycle it will load the new flash code and start up.
If the board loads incorrectly for some reason, it can get a corrupted FPGA file and no longer know where to look for data, at which point you get the continuous beebing. If this happens only MTH with a special fixture for loading files can correct the memory error. G