If a soldier fails his APFT and is flagged, but was never counseled by the CO or his first line within 3 days, is the flag valid?

If a soldier fails a record apft, and the conditions were valid, then the flag is valid. Sure, maybe their leadership failed to take some appropriate steps, but it doesn't invalidate the fact that the soldier failed in the first place.

There is no guideline, however IAW AR 600-8-2 SM should be counseled within 2 days of infraction. So the answer to your question is yes the flag is still valid

Show the Soldier paragraph 2-5 of AR 600-8-2.

2–5. Authentication Unless otherwise specified in this regulation, only commanding officers, commandants, an officer/civilian with specific authority to sign “For the Commander” (for example, BN or higher executive officer, deputy commander, or adjutant), or HQDA general officer principle staff heads or their designee may authenticate a DA Form 268. Failure to counsel within prescribed times does not invalidate the Flag. The Commander, HRC (AHRC–PDV–PS) will authenticate adverse action DA Forms 268 or investigation DA Forms 268 initiated by HQDA.