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What goes wrong

A container change reopened the process

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The process belongs to the product in the container, not to the recipe.

Why the container is in the process

Heat penetration depends on the food, its viscosity and particulates, and on the size and shape of the container and the fill weight. A scheduled process is established for a product in a container, as a pair.

So changing the jar is changing the process

A bigger jar takes longer for heat to reach the center. A different shape changes the path. A heavier fill changes it again. None of those is a packaging decision in isolation.

Headspace counts too

Part 113 defines gross headspace as the vertical distance between the product level and the top edge of the container, and net headspace to the inside surface of the lid. Both are specified terms, which tells you how closely this is controlled.

And initial temperature is a critical factor

Defined as the average temperature of the contents of the coldest container at the time the cycle begins, after thorough stirring or shaking of the filled and sealed container. Fill temperature is part of the process, not a convenience.

Which is why a co-packer has a short container list

They have filed processes for specific containers, and adding one means new process establishment work. That is a cost and a lead time, and it is why the container question narrows quickly.

A larger size is not a simple line extension

Going from a 500 mL to a 946 mL jar is a new process establishment, not a bigger order of the same thing. Budget and schedule it as the former.

So settle the container before the process

Which inverts the usual order in this library and is the right order here. Decide the format you will sell, get the process for it, and then do not change it casually.

References

21 CFR 113.3, the definitions for thermally processed low-acid foods packaged in hermetically sealed containers. Paragraph (j) defines a hermetically sealed container as one designed and intended to be secure against the entry of microorganisms so as to maintain commercial sterility; (n) defines low-acid foods as those with a finished equilibrium pH greater than 4.6 and a water activity greater than 0.85, excluding tomatoes and tomato products below pH 4.7; (r) requires a scheduled process at least equivalent to one established by a competent processing authority. law.cornell.edu
21 CFR part 113 generally, which sets the equipment and procedural requirements for thermal processing systems, including instrumentation, venting, temperature and pressure records and operator supervision for each type of retort. law.cornell.edu
Written from federal regulation, not from a production kitchen. Nothing here is a scheduled process, and nothing here is a substitute for a competent processing authority. If you are considering a shelf-stable low-acid product, the first call is to a process authority rather than to a packaging supplier.