I have been directed here by the Author of Helmod under the statement that apparently this is an issue caused by this Mod. https://mods.factorio.com/mod/helmod/discussion/6822174e79fb5d17956b98e2
Im using helmod to plan out more complex production setups and its especially useful with all the intermediate steps this Mod adds to recipes.
There are just a few issues with Incompability going on.
When in the mod i toggle what Categories of recipes should be visible (Categories available being "Show Disable", "Show hidden", "Show hidden player crafting" and "Show locked recipe")
Sometimes it causes this Error Message to kick me back to the Main Menu:
Error while running event Verbose-Engineering::on_gui_checked_state_changed (ID 3)
Verbose-Engineering/scripts/rocket-silo-circuit-gui.lua:90: attempt to index field 'opened' (a nil value)
stack traceback:
Verbose-Engineering/scripts/rocket-silo-circuit-gui.lua:90: in function 'on_change'
Verbose-Engineering/scripts/rocket-silo-circuit-gui.lua:105: in function <Verbose-Engineering/scripts/rocket-silo-circuit-gui.lua:105>
The Helmod Mod Author has advised me to tell you:
"you can add my comment
he must test the value player.opened ~= nil
local silo_data = storage.silos[player.opened.unit_number]".

While i bring this up i also want to mention that i understand recipes being hidden from player crafting, however having them hidden entirely from the player with the "hidden" variable means it wont show up in helmod or other mods that show for a specific functionality the available recipes at all unless im typing in the recipe name to force it to look up specifically the recipe im after but that requires me to know it already.
It would be better if you use "hide_from_player_crafting" to hide it from the player in the Crafting UI etc. but without giving Mods the impression that it should be hidden at all costs.
"hidden" is more considered as a "hide in every context possible" statement, where as "hide_from_player_crafting" is more like "dont show up in the players UI" kind of deal.
Optionally if desired you can also use "hide_from_signal_gui" and "hide_from_stats" to hide it from signals or stats if this is desired which while affecting those 3 places would avoid giving mods the wrong impression on how to handle your recipes.

Version 0.1.2 should fix the crash with helmod. Thanks for bringing that up!

As for the recipes, all the decompilation recipes already have hide_from_player_crafting as opposed to hidden. The only recipes that are hidden are the number silo crafting recipes, but that's because it randomizes itself after every full craft (the not-hidden rocket part recipe shows all possible options, from which it picks 3). I tweaked some things for Version 0.1.2 in hopes that it would fix the issue you're having, but I would appreciate an example of what you mean so I can better understand what's going on on your end, because right now I'm not really sure what you're experiencing >w<

At the furnace you start the mod with i can smelt for example ore to decompile it in to letters but those Recipes the furnace uses dont show up in helmod unless i choose to show everything thats hidden and then my overview gets poluted with things i shouldnt see and have no use for.
I can see that i take a screenshot next time im int he game to show what i mean visually.

Oh! I understand what you mean. Having all the recipes enabled can make it cluttered when most aren't usable yeah. I didn't even think of that! The fix will be out with the next update, but it may take me a few days since I have to deal with irl stuff. Thanks for bringing it up ^w^

yes something like that, the way helmod does it is it filters them based if they are disabled, not yet unlocked or hidden from player crafting.
generally showing hidden from player crafting is fine as it only adds a few more that are visible in machines but not in the personal crafting UI but enabling disabled or the general hidden ones can spam the UI with a lot of things you arent meant to see or that arent relevant to what your trying to do.
So if the mod only hides a recipe exactly where intended (so as accurate as possible instead of a blanked hidden everywhere) its a lot more convenient to work with.