No one really knows outside maybe a few creators or executives. There are alot of theories and things that have been put forward over the years.
The first appearance of the Simpsons was on the Tracy Ullman show in 1987. In his original appearance Bart wore a blue shirt. When the Simpsons show came out, Bart had an orange shirt. The Simpsons comics first released in 1991 and Bart has had a blue shirt in many but not all Simpsons comics.
Curiously early Bart Simpson merchandise had a Blue shirt, dolls, bart on T shirts, bart in games- although the art for several Simpsons game releases show a green shirt.
One popular theory is they gave the merchandise Bart a blue shirt to undermine bootleggers who might use the orange seen in the show- as “Bartmania” was a thing and the character was quite popular for awhile. There doesn’t seem to be any real evidence to support this though. Another theory has to do with making Bart, the “star character” through the 90’s, stand out since

His sisters also wear orange. A similar theory was that blue is just a generally more pleasant and accepted color, orange has gained popularity and lost it in cycles but it wasn’t a super popular color in that time period and had associations like dated styles of the mid century and 1970’s, prisoner jump suits, and it is associated with Halloween or fall often in America at least. So it could be that from a marketing stand point the blue was just considered more desirable. We could speculate that would explain the use of blue in the comics, by then Bart was popular so they may have wanted to differentiate him as a star in the comics. But that doesn’t explain why they went from blue to orange in the animation, or why they never switched him to blue after the comics and when they were making blue merchandise if their goal was to have him stand out.

Of course it could be any number of mundane things. For example it may have been a supply or cost issue when they started producing merchandise that made it blue. They perhaps didn’t want to change the show character design so instead decided to do comics and all merchandise in blue for branding. It is also possible that the merchandise was based off the Tracy Ullman Simpson sketches and the comics were tied in to the merch.
It is interesting that blue and orange sit across from each other on a color wheel. This could imply a conscious choice or it could imply that somehow somewhere the color just got inverted.
It was (and to a degree still is) common that both animation and merchandise manufacturing were often outsourced to countries with little or no cultural context who had never seen and would never see or know anything about the franchise they were making. Sometimes this has led to various mistakes because either the design details are sent before being finalized so the

product is based off of preliminary drafts and changes are made later that don’t get reflected, or because of QC and other issues that can come up when you are giving instructions across languages to someone who doesn’t know what the final product is,
They just know what is on the instructions.
So it is possible that there is some combination of that at work too.
It is also entirely possible that for legal or creative reasons the creators or IP holders just decided that Bart, again, their most marketable character, especially at the time, should appear differently in media outside of the show. But… ultimately that I am aware of there is no concrete answer as to why Bart has a blue shirt in many comics and most merchandise but orange in the show. It could be as a simple as a mistake somewhere that they ran with- I mentioned the green shorted Bart on some video game art- the Bart in those games usually has a blue shirt, so the green shirt in the art could be a printing error or it

could be that the artists doing the box art either received the wrong instructions or based their box art off of game shots they had for reference and those game shots appeared green. Sometimes that’s all it is. The Simpsons is full of little changes and errors in character design over its run. Some are more obviously intentional like the evolution of the design when you look at the faces of the Simpsons early on vs. Later and some are seemingly animation gaffs like characters hair or eye or skin color changing etc. and it could always be some huge set up- possibly one that is lost to time

As an example-
Marges bee hive hair was chosen to hide rabbit ears! In the Simpsons arcade you can see the ears when she is electrocuted and MG did a comic with rabbits that was his original pitch for Tracy Ullman but he had to create the Simpsons last minute because he didn’t want to give up IP rights for his bunnies. So he’d envisioned marges character going through the show and “at the end” of the run it would be revealed she was a rabbit person. That idea has obviously been made unreasonable as we’ve seen marge without the beehive now- MG said he’d given that one up. Krusty looks like Homer because originally he was supposed to be Homer- the pay off was that Bart and his dad didn’t get along and Bart thought little if his dad but his dad was literally his Hero, Krusty the Clown.
So perhaps they had some idea like that- where blue shirt bart was some alternate universe bart or something like that. We can’t say.

So I am sorry I cannot answer your question but I can give you some theories from over he years.

I remember Bart saying he never had a blue shirt :O Thank you so much for telling that to me- it means a lot :) you aren’t boring like most history books are and your writing is very enjoyable and always makes me happy :$

Lol. Thank you Bensen. I try not to be boring but I’m sure at times I am! I’m glad you enjoyed it though. I’m also glad you’re recovering well and wish you the best.