Daniel,
I assume you disconnected the SmartRF04EB Firmware Downloader from the CC2531 ZigBee USB Dongle after flashing the dongle. Have you tried unplugging the CC2531 dongle, waiting several (say 5?) seconds, then plugging it back into your RPi? Once you’ve tried that, what does the output of lsusb show?
On my my system, I get the following:
[15:46:53] scott@rpi3:~$ lsusb
Bus 001 Device 007: ID 0803:3095 Zoom Telephonics, Inc.
Bus 001 Device 009: ID 0803:3095 Zoom Telephonics, Inc.
Bus 001 Device 008: ID 0658:0200 Sigma Designs, Inc.
Bus 001 Device 006: ID 1a40:0101 Terminus Technology Inc. 4-Port HUB
Bus 001 Device 005: ID 1a40:0101 Terminus Technology Inc. 4-Port HUB
Bus 001 Device 004: ID 0451:16a8 Texas Instruments, Inc.
...
The Texas Intstruments device with ID 0451:16a8 is my ZigBee dongle. Your CC2531 should have the same ID.
I have my CC2531 dongle symlinked to /dev/ttyUSBzigbee using a udev rule:
[15:54:57] scott@rpi3:~$ cat /etc/udev/rules.d/50-usb-serial.rules
SUBSYSTEM=="tty", ATTRS{idVendor}=="0658", ATTRS{idProduct}=="0200", SYMLINK+="ttyUSBzwave", GROUP="dialout", MODE="0660"
SUBSYSTEM=="tty", ATTRS{idVendor}=="0451", ATTRS{idProduct}=="16a8", SYMLINK+="ttyUSBzigbee", GROUP="dialout", MODE="0660"
I had to modify the value of the EXTRA_JAVA_OPTS environment variable in /etc/default/openhab2 so java can “see” both my Z-Wave and ZigBee dongles:
EXTRA_JAVA_OPTS="-Dgnu.io.rxtx.SerialPorts=/dev/ttyUSB0:/dev/ttyACM2:/dev/ttyUSBzigbee:/dev/ttyUSBzwave"
You will have to reboot your RPi after updating the udev rules – more info available here.
Hopefully something in what I’ve provided here will get you going.
Good Luck!