When a batch deviates
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Sooner or later a batch will miss its process. What happens next is written down in the regulation rather than left to you, which is easier than it sounds.
A deviation is defined, not judged
A deviation is any departure from the scheduled process, or a finished equilibrium pH higher than 4.6.
That includes things that feel minor: a fill temperature below specification, a hold time cut short, an acid addition slightly off, a batch held longer than the process allows before filling.
It is not a question of whether the product seems fine. The scheduled process is the standard and a departure from it is a deviation by definition.
The three options
Where a process operation deviates, or the equilibrium pH exceeds 4.6, the processor must do one of three things.
Fully reprocess that portion.
Thermally process it as a low-acid food, which for most small producers is not available because it requires equipment they do not have.
Set it aside for further evaluation by a competent processing authority.
In practice, for a small producer, the realistic choices are reprocess or quarantine and take advice.
What you cannot do
Ship it. Add acid to the filled bottles and call it corrected. Decide it is probably fine because it tastes right and the pH is only slightly over.
And you cannot evaluate it yourself if the evaluation route is the one you are taking, because "further evaluation" means by somebody qualified to do it.
Recording and learning
Record the deviation, what you did, and why. That record is required and it is also the only way deviations stop recurring.
Most deviations in small operations trace to the same handful of causes: a meter not calibrated, a batch scaled without re-validating, an ingredient substituted, or a fill temperature that drifted while somebody was labeling. Each is fixable once it is written down rather than absorbed.