  CO has long been thought to be the best tracer to measure gas masses as it is
readily detected at (sub)mm wavelengths in many disks. Inferred gas masses from
CO in recent ALMA observations of large samples of disks seem inconsistent with
their inferred dust masses. The derived gas-to-dust mass ratios from CO are 1-2
orders of magnitude lower than $\sim$100 even if photodissociation and
freeze-out are included. Herschel measurements of HD line emission imply gas
masses in line with gas-to-dust mass ratios of 100. This suggests that at least
one additional mechanism is removing gaseous CO. Here we test the suggestion
that the bulk of the CO is chemically processed and that the carbon is
sequestered into less volatile species such as CO2, CH3OH and CH4 in the dense,
shielded midplane regions of the disk. Using our gas-grain chemical code we
perform a parameter exploration and follow the CO abundance evolution over a
range of conditions representative of shielded disk midplanes. We find that no
chemical processing of CO takes place on 1-3 Myr timescales for low cosmic-ray
ionisation rates, $< 5\times 10^{-18}$ s$^{-1}$. Assuming an ionisation rate of
$10^{-17}$ s$^{-1}$, more than 90% of the CO is destroyed, but only in the
parts of the disk below 30 K. This order of magnitude destruction of CO is
robust against the choice of grain-surface reaction rate parameters except for
temperatures below 20 K, where there is a strong dependence on the H tunnelling
barrier. The low temperatures needed for CO chemical processing indicate that
the exact disk temperature structure is important, with warm disks around
luminous Herbig stars expected to have little to no CO conversion. For cold
disks around T Tauri stars, a large fraction of the emitting CO layer is
affected unless the disks are young (< 1 Myr). This can lead to inferred gas
masses that are up to two orders of magnitude too low.
