Hello,
I assume Jlink means connecting to JTAG?
If You have repeating resets in a usually running system when connecting JTAG it sounds like there were some watchdog errors.
Not really a surprise when an external debugger is in the game, which is interfering in CPU operation.
We are using FS4500 and to my memory we always activate debug mode prior to using JTAG, because we do not have a CPU-SW snippet running that is acting the Watchdog during JTAG interference.
To my humble understanding this is what the debug mode was made for.