How do you think the IR should be handling the issue of actual Azerbijiani Shia's. We know that they do have a real connection to Iran beyond borders. We also know the Aliyev government is very hostile towards them. I don't believe their are many of them, but they are there.
How does the IR address this issue, how to keep them on our side, while showing teeth to Aliyev government. I think in many cases, IR is very conservative not to lose the support of Azeri Shia's in Shirvan region
Well, this would be a further development of my previous comment's second paragraph (long term solutions).
The first thing to know and insist upon in public communication, is that the only side Iran has ever supported militarily in the Karabakh conflict, is the Azari one. During the first post-Soviet Karabakh war, Iran dispatched IRGC forces to fight alongside Azaris, several were martyred. The reason Iran froze her military support solely lies in the Baku regime's dreams of taking on Iran and separating her Azari provinces, a desire Baku leaders openly expressed in talks with the very IRGC officers who had been tasked to assist them. This needs to be reminded more systematically and brought to the attention of the public in the so-called Republic of Azarbaijan.
Another argument to put forward not just with the religious folk but with the broader public in the Baku republic, is the fact that zionist backing of the Alyiev regime, as contributive to recent military victories over Karabakh Armenians as it may have been, is not stemming from some kind of altruistic sympathy for Azarbaijan but is obviously driven by an ulterior motive, that motive being to use Azarbaijan as a disposable tool in the grand zionist and NATO scheme to destabilize and break Iran apart via "ethnic" separatism. To the religiously-minded, this is unacceptable since it shows how both the Baku regime does not conceive of its military adventures as a confrontation against non-Muslims but it is in fact working towards a much bigger clash with Shia Muslim brethren across the Aras. Others will also tend to question this gamble by the Aliyev regime, because this is no longer a defensive effort but a megalomaniac aggressive policy which, if pursued beyond Iran's red lines, would unnecessarily end up inducing huge costs upon Azarbaijan Republic for the sake of Isra"el" and NATO. The latter are the only parties who'd stand to gain from such a development.
Opposition to the Aliyev clan per se isn't an issue, only military support for Armenia might complicate things in this regard. For the regime itself has numerous opponents including among the less religious, if alone for its high levels of corruption and its repressiveness.
Note that organized groups with ties to Islamic Iran will keep their allegiance intact, because it is ideological and organic in nature. This is more about their popular support base, as well as about the general public in Aran va Shirvan. Now crackdowns against religious Azaris at the hands of Baku authorities - and not just against those who sympathize with the Islamic Revolution, are nothing new. The regime has not only jailed Iran-friendly Islamic activists and clerics, but also imposed a harsh form of secularism complete with hijab bans at certain public venues and education establishments. In this regard, Azarbaijan Republic stands where Turkey used to prior to the AKP's rise to power. This contradiction in the relationship between Baku and Ankara needs to be highlighted more energetically.
Iranian military-grade support for Armenia could offer the Aliyev regime a pretext to step up its repression of religious Shia segments of society, and of pro-IR movements in particular. I specified Shia, because the regime has actually been cultivating salafist and wahhabi currents amongst the Sunni minority in the country's north, in an attempt to establish a counter-weight to pro-Iranian religious forces. The opening of a major wahhabi-oriented mosque in the center of Baku (with Saudi funding if I'm not mistaken) is symbolic of this. Baku is furthermore suspected of having facilitated recruitment of Sunni Muslim volunteers from the Republic of Azarbaijan into terrorist formations in Syria, including "I"SIS. Likewise, we witnessed how Turkey sent Syrian fighters to the Caucasus in order to participate in the previous Karabakh offensive. Relying on such extremists is always a double edged sword, and this represents yet another opportunity for Iran - the rabid shiaphobia of these Syrian armed groups including so-called "moderate" ones isn't lost on anyone. Remind religious Azaris of this fact, reproduce evidence from the archives of the Syrian conflict.
One point which could be raised against the Aliyev regime with pan-Turkist / Bozkurt elements in Baku, is the Kurdish origin of the Aliyevs.
Another option to consider, is promotion of the Azari people's Iranian identity, given that they are "ethnically" Iranian, and culturally as well - with the exception of their language, which is nonetheless featuring fair amounts of Persian vocabulary. Recently, a Hosseyniun official made some statements to this effect. Both religious and less religious citizens of the Baku republic qualify as potential target audiences for Iranian identitarian discourse. Since Azaris are Iranians, Iran is their natural motherland. Therefore, regimes trying to push separatist agendas against Iran cannot be supported. And since the safety of greater Iran is paramount, if it supposes to drive Aliyev's invading forces out of Armenia proper - not out of Karabakh, then this will be a legitimate endeavour.
As a complement to the modest thoughts above, I'd recommend listening to Ra'efipur's analysis on the Azarbaijan Republic from last year: