As described in Section 3.4 of [MR:3540958, arXiv:1602.03715], the completeness of the genus 2 curve database for curves of absolute discriminant $\Delta\le 10^6$ has been tested against other tables of genus 2 curves, including those of [Stoll], and Merriman and Smart [https//doi.org/10.1017/S030500410007153X]. However, as explained on the completeness page, it is only complete within the boxes that were searched, and it is likely that there are at least a few genus 2 curves of minimal discriminant $D\le 10^6$ that are not included (even though no such curves are currently known).
The reliability of specific data associated to genus 2 curves is discussed below.

In cases where the set of rational points has not been provably determined, this is indicated by the label known rational points. In cases where the set of rational points has been provably determined (via some variant of Chabauty's method implemented in Magma), this is indicated by the label all rational points; this applies to about half the curves in the database.

The power of 2 in the conductor of the Jacobian (originally bounded analytically) has been rigorously verified by Tim Dokchitser and Christopher Doris [arXiv:1706.06162] using algebraic methods.

All Lfunction computations are conditional on the assumption that the Lfunction lies in the Selberg class (in particular, that it has a meromorphic continuation to $\C$ and satisfies a functional equation). This also applies to the Euler factor at 2 for curves with bad reduction at 2.

Subject to the assumption that the Lfunction lies in the Selberg class, the root number has been rigorously computed and the analytic ranks are rigorous upper bounds. For 99 percent of the curves in the database the MordellWeil rank of the Jacobian has been rigorously computed using Magma code provided by Michael Stoll; in every case this matches the listed analytic rank.

The data on the geometric endomorphism ring that was initially computed heuristically has now been rigorously certified by Davide Lombardo [arXiv:1610.09674] and by Edgar Costa, Nicolas Mascot, Jeroen Sijsling, and John Voight [arXiv:1705.09248], independently, by different methods. This rigorously confirms the SatoTate group computations (the fact that these independent computation agree is a consistency check).

Isogeny class identifications are based on a comparison of Euler factors at good primes up to $2^{20}$. Jacobians that are not identified as members of the same isogeny class are provably nonisogenous, but the identification of membership within a particular isogeny class is heuristic (except for Richelot isogenies, no explicit isogenies have been computed). In principle it could be made rigorous in any particular case via a FaltingsSerre argument, as described in [arXiv:1805.10873], but this has only been done for a handful of cases such as the isogeny class of conductor 277.
All invariants not specifically mentioned above were computed using rigorous algorithms that do not depend on any unproved hypotheses.