It's not entirely clear, but it seems like her ties to the Order were strengthening
Dave Filoni discussed his intentions for the unfinished episodes in a 2016 interview with IGN:
What was significant about that was that it was the story that was really going to draw her possibly back into the Jedi Order, because the motivation around this conflict with Maul was her knowing the personal history between Maul and Obi Wan
[Ahsoka] was actually planning with Obi Wan and Anakin the capture and attack that would get them Maul, because she had figured out where he was towards the end of the Clone War. But before they can go through with this plan together, Obi Wan and at one Anakin get called away to Coruscant to save the Chancellor, which leaves her with Rex – and some other exciting characters – to basically go and deal with Darth Maul, once and for all.
So, according to Filoni, Ahsoka's involvement went something like this:
- While out doing her own thing in the galaxy, Ahsoka somehow uncovers intelligence on Maul's whereabouts
- She reaches out to Anakin and/or Obi-Wan with her information
- For some unknown reason, the Jedi involve Ahsoka in the plan
- Anakin and Obi-Wan are called away on more urgent business1
- Ahsoka carries out the mission alone (albeit with Rex and a bunch of clones)
Some of this was incorporated into the canon novel Ahsoka (emphasis mine):
She'd walked away from the Jedi Temple with nothing but the clothes on her back and had struggled for a long time to find a new place in the galaxy. When she had found a mission, when she had reached out to her former master for help, he had reached back and given her the Jedi weapons to do the job.
If Filoni's plans are to be taken as canon, the most likely explanation is that Ahsoka was given authority over a contingent of clones (including Rex) as part of a soft return to the Jedi Order; perhaps the Council wanted to draw her back into the fold.
What is clear, however, is that Ahsoka had no formal position in the Grand Army of the Republic; this is mentioned explicitly in the novel:
She wasn't a commander anymore, even though the battalion still treated her with the same courtesy they always had, because of her reputation.
1 Wookieepedia speculates that this was the mission in the prologue to Revenge of the Sith; I'm not sure if that's substantiated but, given the timeframe (Order 66 occurs while Ahsoka is fighting Maul on Mandalore), it seems plausible.