RQA GLP Committee
It would depend on your processes and how you separate them out. It would be useful to check the run had completed successfully when the results were available. It would be possible to extend your audit over a couple of days to include a look at the final integration, calibration lines, controls, carry over etc. if the audit comprised the who analysis. In a process based inspection you could split your audit types down to sample preparation, sample loading, sample integration, raw data audits etc. Take snap shots of all the different procedures until you build a full picture.
Audit of the data could be carried out at any time during the duration of the study, particularly if it is a long term study (over a year) then it would break the audit in to manageable chunks and also alert you to any issues before the study was in the reporting phase. Conduct a risk assessment looking at the criticality of the data and what impact it would have if a problem was not detected early on in the process and base your decision on that - document your decision as justification.
How you do this should be driven by your SOPs and a risk assessment should be done to ensure that data that had previously been reviewed was not re-checked, and that nothing had been missed between audits.