Interesting, you should report that as a bug to the Factorio bug report forum (if it's not there already). Mods don't have any control over the save/load process, and they certainly can't corrupt save files.
General warning though: Mods (especially script mods with persistent data) don't go well with the map editor at all. IIGC the editor will always clear all saved mod data when editing existing saves, because doing anything else with the data is sure to make mods unstable if the entities they depend on are messed with. If you edit a map with existing factory buildings, you'll find they don't work after reloading the map.
