The log files are stored on the RMX harddrive, while the software images are stored on a 1G compact flash drive. Deleting the logs will not free up additional space on the flash drive for loading an upgrade package. These error messages are most commonly caused by a failed upgrade which leaves a partial .bin file on the compact flash. If a reboot does not clear the error, then the next step is to try doing the upgrade over LAN 3, as that often resolves these issues.
To access the bridge on LAN 3, you set your PC IP address to any address on the 169.254.192.0/24 subnet (169.254.192.100 for example) and connect it to LAN 3 on the RMX 2000 (strait or crossed cable will work, the port is auto-sensing). You can then access the RMX web GUI at 169.254.192.10, and try the upgrade from there. If that does not work either, then call polycom support at 1-888-248-4143 and open a ticket on your RMX to work with one of our agents, we can figure out what is filling up the compact flash and clear it out.