I have a similar problem but I don't think it is solely related to debug (I'm using a K40 on a KwikStik).
I have a PDB that triggers ADC0 and then samples are stored to a buffer with DMA.
The only time the CPU gets involved is when a buffer is full and the DMA interrupts the CPU to tell it to get the data.
This process runs fine as long as there are no interruptions.
Either if the code takes too long or a breakpoint is encountered in the debugger, the digitizing process locks up and I can't figure out how to restart it programmatically.
When it stops, PDB0_CH0S = 0x10001 (channel 0 sequence error) and I can't seem to clear it.
The ADC and DMA modules are not showing any errors, but the ADC0_SC1[COCO] bit is 0.
I have the PDB0_SC[PDBEIE] bit set and the ISR tries to clear the sequence error bit by writing 1 to it in PDB0_CH0S.
It also clears the PDB0_SC[PDBIF] bit by writing a 0 to it.
(One other question is that in the K40 Reference Manual (K40P100M100SF2RM) section 35.1.6 (Mode of Operation in the PDB chapter) lists a Debug mode, where the counter is paused when the processor is in debug mode. There is no explanation of how to set the PDB into Debug Mode, but this would help).
Regardless, once I'm in this locked up state I can't get out of it without restarting the processor. What do I need to do to get it started again?