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If you want to know the math, if you expect to produces N seeds, the error on your estimate will be around the square root of N. (maybe I'm off by a factor of 2)
So just crafting the recipes straight, you will randomly deplete your seed stocks from time to time. Especially if some of your fruits and nuts spoil or get burned as fuel.
To solve the problem, use a productivity bonus when processing fruits and nuts. The Biochamber has an intrinsic +50% bonus. If you don't use them, you'll need productivity modules to get a positive feedback loop for seed production.
Are you under using the jellynuts in your line and storing the produce in chests before they get turned into jelly and tons of them are rotting away?
Do you have an inserter for jelly not filtering for seeds and it randomly tosses them on the line every now and then and they get burnt somewhere on the end?
Seeds just get put on the incinerator belt with everything else (except bioflux and nutrients). Splitter to take seeds off, priority splitter to merge seeds back on if they back up.
None of these fancy circuits!