Those warnings would indicate to me that the flash's calibration region is corrupteded or empty. (This region currently just stores the VCTCXO trim DAC value and the FPGA size.)
Were you seeing these warnings previously? If not, when exactly did you start seeing them, and could you detail the process that led to this?
If you look at the help text for the bladeRF-cli command, 'flash_init_cal' you will see how to restore these. However, you will need to know the factory VCTCXO trim DAC calibration value, which you may have previously backed up or have in logs. (It would be in any output from the bladeRF-cli "info" command.) For example, with an x40 and a VCTCXO trim dac value of 0x8000: 'flash_init_cal 40 0x8000'
If you don't have your VCTCXO trim dac value, you could try emailing bladeRF@nuand.com
with your device's serial number (also viewable from the bladeRF-cli 'info' command) to see if it is on file.
By the way, could you just make note of the libbladeRF version you have? (bladeRF-cli's "version" command output would suffice.) I'm assuming you're on 1.0.0?