if you're scared of this happening, you can always try my awesome ass-backwards backup method that i use for the old EMS carts-
Back up the cart in question to a Mega Memory Cart, then restore that SAV to a USB cart and pull the SAV off that onto your computer.
Or, in your case, use the SmartBoy reader to pull the SAV off the MMC once it's saved to. 
Might help avoid whatever issue is occurring between the cart and the reader.
However, I'd take a look at kitsch's method first before trying this- if the resistor is gone, then I doubt my method will help at all.

in what way is the cart corrupted?

do you perchance have a bunch of "1A"s displayed on the main screen? 

there's a couple recurring issues with the cart, more details would help. 

also, if you've opened up the cart's case recently, i would almost assure you the 10k resistor at the top snapped off.  R1 i'm pretty sure...  its 10k and 0603 package.

I have 2 non-USB Bleep Bloop carts and a SmartBoy reader. Recently whenever I try to back up one of my carts, it crashes. The result is my cart is corrupted and I have to load up a .sav from 2009

Any help or advice would be much appreciated and I apologize if this has been brought up before in another thread.