The European Space Agency (ESA) Gaia satellite has 106 CCD image sensors which will suffer from increased charge transfer inefficiency (CTI) as a result of radiation damage. To aid the mitigation at low signal levels, the CCD design includes Supplementary Buried Channels (SBCs, otherwise known as `notches) within each CCD column. We present the largest published sample of Gaia CCD SBC Full Well Capacity (FWC) laboratory measurements and simulations based on 13 devices. We find that Gaia CCDs manufactured post-2004 have SBCs with FWCs in the upper half of each CCD that are systematically smaller by two orders of magnitude (<50 electrons) compared to those manufactured pre-2004 (thousands of electrons). Gaias faint star (13 < G < 20 mag) astrometric performance predictions by Prodhomme et al. and Holl et al. use pre-2004 SBC FWCs as inputs to their simulations. However, all the CCDs already integrated onto the satellite for the 2013 launch are post-2004. SBC FWC measurements are not available for one of our five post-2004 CCDs but the fact it meets Gaias image location requirements suggests it has SBC FWCs similar to pre-2004. It is too late to measure the SBC FWCs onboard the satellite and it is not possible to theoretically predict them. Gaias faint star astrometric performance predictions depend on knowledge of the onboard SBC FWCs but as these are currently unavailable, it is not known how representative of the whole focal plane the current predictions are. Therefore, we suggest Gaias initial in-orbit calibrations should include measurement of the onboard SBC FWCs. We present a potential method to do this. Faint star astrometric performance predictions based on onboard SBC FWCs at the start of the mission would allow satellite operating conditions or CTI software mitigation to be further optimised to improve the scientific return of Gaia.