This answer is going to be a bit speculative, since no official reason has been given, as far as I can tell. Obviously, the embargo is a form of pressure on the Kurdish-controlled areas.
First, as a bit of background, relations between the Kurdish enclave and the Assad regime have always been uneasy, as this 2017 Reuters article explains, involving checkpoints blocking some supplies now and then.
Assad’s government trumpeted the defeat of rebels in Aleppo as his greatest victory of the war so far, the return of state control to a city that was once the country’s biggest.
But he has made no move to regain Sheikh Maqsoud, which sits on a hilltop surrounded by areas held by the army.
There is no military presence around the district except a Syrian army checkpoint on the road in. Many government workers and students inside Sheikh Maqsoud commute daily into the city.
Still, Asayish leaders there complained to Reuters that government checkpoints hinder the movement of goods and services into Sheikh Maqsoud. [...]
Mohammed Ali, the head of the Asayish in Sheikh Maqsoud, was very critical of the Syrian government, saying it often obstructed passage between Sheikh Maqsoud and other areas, blocking humanitarian supplies.
Second, Assad is well-known for overwhelmingly prioritizing regime-friendly areas for rebuilding following the war, showing that he essentially doesn't give two hoots about the others Syrians.
reconstruction has taken place unequally,
sometimes in the same city. For example, in many
eastern neighborhoods of Aleppo recaptured by the
regime and its allies in December 2016, the government
has made no efforts to enhance living conditions or
rebuild residential areas; in such places, the provision
of state services has been minimal. The renovation of
war-ravaged buildings has been almost entirely done
and paid for by the inhabitants themselves.
Notably, these were the same places that tended to be
more damaged in the conflict. For instance, although
most of the destruction in Aleppo took place in the
eastern part of the city, which had been under opposition
control, eight out of the fifteen “priority areas” the
government identified for reconstruction at the end of
2017 were in the western and central parts of the city,
where there had been less overall destruction and where
infrastructure and public services were better. In Homs,
too, the reconstruction or rehabilitation of buildings
was prioritized in districts whose inhabitants historically
favored the regime, not in the most damaged areas
formerly under opposition control. The same has been
true in the Damascus suburbs of Eastern Ghouta, which
the regime recaptured in the spring of 2018. As of the
summer of 2019, little reconstruction or rehabilitation
had started there.
Furthermore, the land and buildings (or whatever was left thereof) of those who fled abroad were confiscated by various decrees.
And besides unofficially taxing external aid funds by crooked exchange rates, Assad also resorted (at least from 2019 onwards) to wealth confiscation from businesses and oligarchs who had been somewhat regime friendly, essentially in a worsening dog-eat-dog economic situation. (These steps were done under the official mantle of an anti-corruption campaign.)
Nonetheless, this year,
Food prices are spiralling out of control. A kilogram of green beans has reached 23,000 Syrian pounds in some areas - almost a quarter of a monthly state salary. [...]
As the first few days of Ramadan pass, Syrians in government-held areas are faced with an unprecedented increase in the cost of living. Estimates from the Syrian economic think tank Kassioun reveal that for an average family in March/April 2022, the monthly cost of living is estimated to be around 2,860,381 pounds, an increase of 833,405 (over $200) since January.
And lastly, there's some talk of food shortage this year, following the war in Ukraine:
Abdul Latif al-Amin, director-general of the Syrian Grain Establishment, said authorities are attempting to compensate for the shortage of wheat by encouraging the manufacture of semolina, pasta, bulgur and other foodstuffs. [...]
Yet, Syrian grain and wheat supplies - which come mainly from Russia - are reportedly fine, with the Ministry of Internal Trade and Consumer Protection stating that current stocks are acceptable without reaching a supply danger zone.
Of course, it's hard to be sure which of those statements regarding supplies is correct, in a country like Syria. But the food (including flour) embargo on the Kurdish enclave appears related. Of course, it might have been just a pretext as well.
It's also worth noting that there was a somewhat similar bread crisis in the March last year, which Western human-rights organizations say was largely engineered by the Syrian government, when it then decreased bread subsidies:
“Syrian officials say that ensuring everyone has enough bread is a priority, but its actions show otherwise,” said Sara Kayyali, Syria researcher at Human Rights Watch. “Millions are going hungry in Syria, in large part because of the government’s failure to address a bread crisis it helped to create.” [...]
The Syrian government provides subsidized flour and fuel to public bakeries, which then sell subsidized bread. In September, Syria’s State News Agency, SANA, announced a new formula, limiting the amount of government-subsidized bread people can buy based on family size. On October 29 , the Syrian government doubled the price of the subsidized bread.
And as with other forms of aid, subsidized bread too was given on politial considerations
Residents also described discriminatory distribution. In some areas, there are separate lines for the military and security personnel, for residents, and for displaced people, who get the lowest priority. A report by Newslines Institute says that Syrian security services interfere in bread and wheat distribution, including taking bread from bakeries and selling it on the black market.
And again there was unclarity regarding imports
from mid-2019 until February 2021, the Syrian government was unable to procure wheat from outside, given alleged government “funding restrictions.” Syrian tenders for wheat in 2019 and 2020 have primarily requested Russian-sourced wheat. But Russian government-imposed restrictions on wheat sales during the Covid-19 pandemic have made it difficult for countries to procure wheat from Russia, even military allies. It announced a 7 million ton limit on exports of wheat and other grains to other countries in April 2020 and that it was extending these restrictions in November.
On February 26, 2021, government-affiliated news outlets said that wheat is being imported from Russia, as part of a million-ton deal, although no official source has confirmed this.
according to the United Nations, Syria's wheat harvest last year  was at its lowest in 50 years, and was less than half of what it was in 2020.
And in Feb this year they announced some new forms of rationing.
Syria is set to ration its reserves of wheat and other essentials and basic goods, in a range of measures to brace against the shortages and major supply issues predicted to result from Russia's invasion of Ukraine.
The announcement was made on Thursday by Syria's Council of Ministers, which cited the need to ration basic goods such as wheat, sugar and cooking oil. The Council also said that it would limit the regime's public spending, as commodity prices around the world are expected to rise significantly.
One could venture a guess that rationing, like reconstruction, would be applied unequally to regime friendly areas vs the less friendly ones.