I use the same IDE but with Linux Mint 19.1 (based on Ubuntu 18.04 I think)
I had similar problems with Nano BLE 33. The native USB used for programming interrupted the USB link at the PC. That switched to the next free ttyACMx.
Because I use more BLE 33 at the same time (with different projects in the same workspace) I do not use the embedded serial monitor but several instances of GtkTerm. No problems any more. Only you have to reconnect the terminal (key F5) after flashing the board. The ttyACMx connection is stable.
By the way, I start the different instances of GtkTerm with different configurations (different background colors and ttyACMs) via Run->External Tools from Eclipse.