A flag $C_0 \subsetneq C_1 \cdots \subsetneq C_s \subsetneq {\mathbb F}_q^n $ of linear codes is said to be self-orthogonal if the duals of the codes in the flag satisfy $C_{i}^\perp=C_{s-i}$, and it is said to satisfy the isometry-dual property with respect to an isometry vector ${\bf x}$ if $C_i^\perp={\bf x} C_{s-i}$ for $i=1, \dots, s$. We characterize complete (i.e. $s=n$) flags with the isometry-dual property by means of the existence of a word with non-zero coordinates in a certain linear subspace of ${\mathbb F}_q^n$. For flags of algebraic geometry (AG) codes we prove a so-called translation property of isometry-dual flags and give a construction of complete self-orthogonal flags, providing examples of self-orthogonal flags over some maximal function fields. At the end we characterize the divisors giving the isometry-dual property and the related isometry vectors showing that for each function field there is only a finite number of isometry vectors and that they are related by cyclic repetitions.