While there is not an official polity on this, proper military etiquette would expect that sailors engaged in Physical Fitness activity would stop the exercise, observe colors, and than continue.
It would be expected that any highly strenuous activity would start far before or immediately after colors.

References:
– Command Fitness Leader Guide One, Section 3, Page 13

COs are authorized to grant a member who “failed” the PRT one retest of a complete PRT portion only during the current PFA cycle. A BCA “Bad Day” is not authorized. COs are encouraged to establish their “Bad Day” policy within the PFA Notification (10 Week Notice). If the “Bad Day” policy is not already established, the member must request the “Bad Day” in writing within 24 hours of completing the PRT. If approved, the retest must be administered within seven days of the initial PRT failure and within the same PFA cycle for which the “Bad Day” was requested. (Drilling reservists must retest by the end of the following month, not exceeding 45 days from the BCA date.)

All portions of the PRT must be retaken. If authorized in the 10 Week Notice, member may utilize the alternate-cardio option for the “Bad Day” retest. If the individual is approved for a “Bad Day” but does not participate in the retest, becomes “medically waived” before the retest, is injured during the retest or transfers to another assignment before the retest, the initial test score is to be entered into PRIMS as the official PFA.

In other words, the original PFA scores will remain valid until the PRT “Bad Day” scores from the retest are entered in PRIMS. If the member passes the retest, the CFL will update the data in PRIMS