Perhaps you have activated the electronic shutter. Use the mechanical shutter for flashing.

I recently got this used camera from eBay. when I first got it the flash was working just fine. I would pop it and it'd be on auto and it would work. Now I can't seem to get it to work. I pop the thingy on the side and this icon pops up saying that flash is off. So I go to the settings (I've tried this with every mode on the wheel spin thing) and I go to the menu section where I can choose flash settings but it's non accessible. It only lets me change the Red eye removal setting. What's going on? Do I need to update the firmware? Did I get a faulty camera?

Have you considered the many 150mm - 600mm options? Fujifilm offers one that does work with both the 1.4x and 2x tc. If you want one that has brighter f-stops, then Tamron and Sigma offer them in various mounts. You can pair them with oh, say a Fringer smart adapter (or one of Fringer’s competitor’s smart adapters) and get aperture dial control as well as having correct EXIF stored in the images. There are plenty of reports these adapters work with teleconverters, I suppose you can write the adapter’s manufacturer and ask if it matters if you use camera -> xf tc -> adapter -> lens or camera -> adapter -> native lens tc -> lens. Depending on the budget, you may be able to find a setup in the new or used market you like.

Are any other settings reverted back to a default state as well on restarts? Also, are any other MF Assist options reset back to the split image state when the camera is restarted? If these happen, it could be a hardware problem, as in if the first answer is ‘yes’, the chip storing the settings or the “back-up” battery is bad. If the second answer is ‘yes’, the cell in the chip holding that setting’s storage area may be bad. Based on what you and @Greybeard are saying, it does not sound like a general firmware / software issue, it could still be a firmware issue just for this camera — the firmware update just did not install all the way.

I'm currently using the 70-300 plus the Fuji 1.4x teleconverter for nature photography. I can usually get the final results I want by upscaling and cropping the image. I would like to have more focal length up front. So I started looking at the  Fujifilm 100-400, then the Sigma 100-400. After comparing the two, the Sigma won except for one thing- my fuji teleconverter is not compatible and according to Sigma support they have no plans for creating an xMount teleconverter- which is a deal breaker for me because there are times I will want more magnification that the 100-400 lens alone can offer. I mean, if I'm going to spend $800 on a lens I want to be able to realize its full potential. I'm wondering if other Fujifilm X camera owners have been in a similar conundrum. If so what would you recommend? Stick with the 70-300 + teleconverter? Look at 3rd party manual lenses? a used DSLR lens?