Ran both good and discolored bottle contents through filter paper, nothing on the filter paper. All ingredients are 100% water soluble.
Ok, so this suggests that either nothing has precipitated out of solution, or if it has, it's too small to be caught by the filter paper. The cloudy appearance suggests to me that something is scattering the light, and is therefore probably in a solid rather than liquid phase. What grade filter paper did you use, and do you have any finer ones available?
Also note that, whilst the ingredients are nominally all water-soluble, the effect of combining them can do interesting things - for example, forming new compounds that are less soluble, or reducing the saturation point such that part of the content of something may cease to be soluble.
What is the water source used for the product?
Is it blended in one big tank prior to packing, such that you'd expect it to be homogeneous before filling?
Yes,tank has stirrer to ensure homogenous mixing throughout the run
Filtered potable mains? What sort of filter? May be academic in this case, but can have a bearing in some circumstances, with certain weirder occasional issues with soft driks products.
Any analytical differences between the good/bad bottles - e.g. Brix, acidity, pH?
pH of good bottle 4.7
pH of discolored bottle 4.3.... so not much difference.
That looks like a fairly notable difference to me. Are you able to measure titratable acidity? The results imply that the acid content has increased, which makes me wonder about e.g. lactic/acetic acid production by bacteria.
When are the microbiological results due?
We ran no added sugar flavour before this batch and there is no issue with no added sugar batch. Only difference between this and no added sugar batch is the additional sugar otherwise rest all ingredients are same, can addition of sugar make liquid unstable.
Is the sugar just standard sucrose? If so, I wouldn't expect this to have this type of impact. With glucose you can occasionally see formation solid crystals if the glucose content is high, particularly if the product is subjected to repeated changes in temperature. Given what you've said about the drink, I wouldn't have thought this is likely here though.
Still don't get it why some bottles are good and others bad and that too in same box.
This is the pattern throughout the run which rules out that may be something happened at start, middle or end of the run.
What is your filling setup? e.g. is this a multi-head filler?
I've seen issues where there is a subtle issue with one head in a multi-head unit, resulting in micro problems with a proportion of bottles spread throughout a batch. With some types of issue it can even be the case that not every bottle from the "bad" head is affected, making it even harder to spot the pattern and diagnose the actual issue.
Is there any post-fill processing, e.g. bath/tunnel pasteurisation?