The "limit" you speak of is the minimum amount of writes to a flash memory before "flash senility".
Because of the way the flash memory works, some bits inside the memory card might become invalid, and become unwriteable. The card controller or reader/writer then isolates the whole memory block containing that bit (1KB, usually), and the card loses that much capacity.
You can still continue to use that card, but more and more faulty bits will pop up with time. This is called "senility".
This happens when you write to the card, so it can't corrupt the data. If the writer sees it can't write to a particular bit, it decides the bit's invalid, and isolates it.
The actual limit at which the senility occurs is about two to three times the declared number, because of a huge safety margin.
The limit is usually very big. Don't worry, a single game can't reach it. Or more games, for that matter.
Flashcards have the declared limit because the memory is built-in and can't be replaced. The M3 is an adaptor type card, where you use a replaceable memory card. I don't think the limit applies to it. Since the saves are written to the memory card, the "limit" is the limit of the card, not the M3.
And the life of a memory card is so long, you'll sooner buy a bigger memory card than reach the read/write "limit".
More about flash memory
here
Don't worry, be happy