Of course this is an estimate based on the script, the plot details, and basic guess-work.

Episode 1: 1 Day

According to the script, the first we see of Yaz and the Doctor after the opening, its 12:50. Then the final scene takes place the next day at 12:07. So lets say roughly 1 day (multiple times they have issues with the TARDIS).

Episode 2: 1 Days 6 Hours

Day 1 - They arrive, Yaz and Dan disapeer, Mary and the Doctor follow Svild back to the base.

Day 2 - The Doctor meets with Skaak, the battle occurs, and at the end of that day they blow up the ships, the Doctor gets Dan and they go to Atropos

Episode 3: 3 hours 3 minutes

According to the script, on Atropos they spend 1 hour 22 minutes on Time. Then an 8 minute trip to Vinder's home. Then 1 hour 33 minutes in the TARDIS before the Angel jumps out of Yaz's phone. In this hour the Doctor records the hologram for Yaz.

Episode 4: 43 Minutes

Its essentially a siege story in Jericho's basement, and the script suggests around 43 minutes. Probably one of the few episodes to be more-or-less in real time for her.

Episode 5: 5 hours.

That is at Division though, and she might've spent more time in the weeping angel form.

Episode 6: 3 hours

Roughly 1/5 of this episode the Doctors are one. For the rest of the episode, the Doctor experianced 3 different memories at once, so that is 48x3=144 minutes, so about 2 hours 24 minutes. But there is a small time skip, so lets round up to 3 hours

Overall

So at a minimum (it is likely more given multiple time skips, and the inevitable adventure taking place in between moments like when they go from Atropos to Medderton, or while the Doctor is an Angel)...

Flux for the Doctor takes place over 66 hours (rounded up). 66 hours no sleep or rest where she experiences a doomsday event, becoming a weeping angel, meeting a past companion, discovering more mysteries surrounding herself, meets her abusive adoptive mother, and eventually growing as a person by moving on from all that grief.