Sometimes, when you add the mod to an existing game, and you've already researched the technology, the game will not realize this and not automatically enable the recipe. Sometimes it does enable it. Not much I can do about that besides rewrite the system in a control script in every one of my mods to make sure the game is properly trolling the tech tree every time someone adds a new mod, which introduces new points of failure in every one of my mods, and so is something I feel instead needs to be handled in the core game.
How about a migration script? You know what technologies your mod(s) depend on, what unlocks what, so you could soft-reset these technologies with something like this:
local technologies = {"tech_1", "tech_2"}
for _, force in pairs(game.forces) do
for _, tech in ipairs(technologies) do
if force.technologies[tech] ~= nil and force.technologies[tech].researched then
force.technologies[tech].researched = false
force.technologies[tech].researched = true
end
end
end