Dear Dave,
Now that can be done. But if we check the product microbial load periodically (suppose once in a week) and in one test we found product positive in pathogens than the products from last whole week will be in question. As this positive pathogen test might be faileure in sanitation or malfunctioning of any eqipment and we will not know from how long it started.
I presume you are referring to a zero tolerant (ZT) pathogen species.
Well, if yr process / supplier are appropriate, the results should be negative ?? If not, and yr environment is appropriate you have probably verified that the COA is incorrect (eg, fictional or [more likely] the sampling is inadequate to detect contamination [as is common]).
If a positive result, several options can be considered, (a) one corrective action (before the problem) is to use, for example, daily lot codes and re-sample (increased sample) the problem day(s). And/or reject back to yr supplier / change supplier, (assuming you trust yr own environment).
Or (b) you can simply trust to luck and re-sample the original 1-week batch. The laws of sampling are (usually) on yr side.

Admittedly, yr results hv now
proven the likely continuing existence of a ZT pathogen in the lot so you may consider re-sampling unethical although it is a commonly utilised principle, yr opinion may depend on the specific situation also, eg product risk status, history - two successive detections is perhaps rather different to once in 5 years. You can find proposed sampling schemes in the microbiological literature, eg ICMSF (the work involved may well be substantial / expensive). Or © perhaps the simplest, reject the relevant lot of raw material back to the supplier, this assumes item / lot identification is possible. Of course, the supplier may only co-operate if his
delivered goods are specifically tested. Sometimes a question of leverage.
Another comment is that, we produce cup cake dry mix (powder) which is not ready to eat. It will require preparation. I guess according to FDA regulation we need to have microbial checking if the prodcut is ready to eat.
If yr question is whether finished product which is ready-to-cook is different to ready-to-eat, ie has a different risk status, obviously yes (and particularly from a regulatory aspect).
Basically our process does not have any step to get control on micro. We bring raw powder material in and blend them and pack them. The only way we control micro is by COA from raw material supplier.
The point is that, from the consumer's side,
you are responsible for the final quality / safety, not yr supplier. Therefore you hv to act accordingly.
Rgds / Charles.C