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Maybe try resetting sp (stack pointer register) to 0 to make sure you're working with "empty" (at least logically) stack at beginning of program?
By references you mean reference ID of objects? I've yet to use those, I handle it with sbn/lbn and fixed names, that way even if reference changes, program still works. Although I don't think references should change, but I've never tested that.
I've yet to see an actual reason (outside of trying to write your own AI, idk) to have more than 128 lines in single chip. In almost all cases you can separate logic into multiple chips and have them interact with each other. It's enough to do a lot of stuff from controlling a furnace to aligning dish if you have a separate chip doing just that.
P.S. or maybe I'm too new to this and haven't encountered that problem yet.
Having played with stacks a bit, I found it easy to mis-manage these things.
About the stack, above is correct, sp 0 helps. (strange but ok)
JeanDeaux, yes if you not set stack sp 0, you get stack overflow.
if you push a value and “restart” IC10 sp-pointer is not 0
Another "glitch", If place IC housing between two frames, the game tick works differently at the code level. In minecraft there was a similar bug between chunks when redstone didn't work. But this glitch is cured with yield if you don't reach the number of instructions to the limit per tick.
128 of is not enough to handle all the errors. I have to ignore some possible errors, and then half my base explodes after the update :D
https://steamcommunity.com/app/544550/discussions/2/4406292251590450431/
I am not seeing updating issues in any of my programs that you are describing; so this is not a shared experience. My programs have steadily worked through every upgrade without any issues at all. I would tend to favor an opinion that it's your coding methods that are not handling re-starts with currently running equipment that is more likely at issue.