I'm not sure how you mean by SD card. There are no cards or anything else that you need to take out of the machine.
It sounds like you have either a flash drive with wrong format, or your files are still zipped, maybe.

You want to make sure you download the updated code file from the Stern website onto your desktop (not the read-me file, which is there only to read the new and previous code updates). You will see the file folder contains 3 files. You want them all. Highlight that file folder on your desktop once downloaded and unzip or "extract" those files again on the desktop...all the above takes anywhere from 15 to 25 minutes. Once extracted/unzipped, drag the files into your flash drive. This again will take 10 or 15 minutes probably.
Make sure your flash drive is formatted FAT32 (similar appearing formats, like ExFAT, will not work). You can check this formatting ususally by clicking "properties" on the flash drive once it is in your computer. Note, the company PNY, which you can get at your local tech store or Best Buy come formatted this way...companies like SanDisk are not. Also note many folks, including myself have had issues downloading from Mac, and thus many including myself have had success with Windows computers.
Once the files are transferred, with the pinball machine off, place your flash drive into the recommended usb port behind the backglass and turn the pinball machine on...you will be prompted to update. There are a few options and likely all are fine, but I choose Full update and Yes to Verify. Best i can tell, Full vs. Quick is complete code revamp vs. Just the new changes and the verify is to analyze the flash and files for corruption or unnecessary files. Once finished, turn the pinball machine off and remove the flash drive. Thats it. Next time you turn it on, it will show you the new code is installed.
Note, a few folks, including myself encountered "fail to update" when in the process of the pinball updating...just try again, (the pinball machine screen usually takes you back to the initial screen asking if you want to update, full, verify, etc.)...just try again and it should work. For some on occasion, I noticed they needed to re-download from the website>desktop>flash drive a second time and that eventually worked as long as formatting was correct.
Once update is done, you will need to re-modify settings, i.e. free play, ball eject speed, etc..

Hope that helps. It's an awesome game! Seriously addictive!!!

Great question! And thank you. I tell ya, if it does have an SD card I didn't know about it or ever had to mess with it. I'll have to check into that bc I'd love to be able to backup a code if I update and theres issues with updated code (perfect example being the recent . 92 ramp issue...would have been nice to just be able to more simply revert back to .89 without having to re download from the Stern site). But thus far I've been able to update 3 times (.92, back to .89 and now .93) without ever messing with an SD card. Fortunately, I have not have any major issues with anything and the game has played well all along the way. But from your statement, I will definitely go hunting for this card, bc as mentioned, it would be nice to have a backup of prior code if newer code is under par. I havent heard anyone else talking about this card. Where is this card located anyway?