Does anyone know anything about dissociation of boronate ligands from agarose beads?
Can it be prevented / reduced?
Is there an equilibrium?
Would adding free boron help to shift the equilibrium?
Can the ligands reassociate?

The formation of the "complex" (the product is actually a moderately stable compound involving covalent bonds) between boronate functional groups and analytes containing cis diols is quite pH dependent. Generally, the pH should be greater than 7.5 to promote formation of the adduct. In general, the stability of the adduct is maximal at pHs between 7 and 9. Hydrolysis of the adduct occurs under both acidic and basic conditions. So, you can maximize the stability of the adduct by keeping the pH in the optimal range. On the other hand, if you're referring to loss of the boronate group itself from the gel, this process is effectively irreversible. The boronate group is not super stable and is subject to oxidation. I would try excluding oxygen from samples and eluents as a means of minimizing oxidative damage. Another alternative might be the addition of a reducing agent such as sulfite to the eluent.