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It's actually been bugging me for a while, and I've not reported it as I've not been sure if this was the issue or not. But I just confirmed it.

I had a full research queue, the game autosaved, I quit then loaded again, only the currently researching technology was loaded.

Are you using any mods? Because I can't reproduce any issue with the research queue.

After further testing, it only seems to do it when something changes in my mod.

perhaps it could be on on_configuration_changed, or maybe if it's when I call reset_technology_effects() (one of my mods does this on on_configuration_changed)

either way, when I add a new item, or change a recipe etc, the queue clears.

Ok, I found the issue: reset_technology_effects wouldn't preserve the research queue.

Thank you Rseding.