Something should be protected by something else

Question

How do you interpret this sentence:

Any change to EEPROM in the field should be protected by transactions."

1. We must protect EEPROM and prevent transactions to change it.

or

2. Transactions must protect EEPROM and prevent changing it (by something!)

Answer 1

Neither is quite right. change is the subject of the sentence, and it is therefore the thing that is being protected. by transactions is an adverbial clause which answers the question "How?" — the method by which the change is being protected. Nothing is said about preventing changes. So to rephrase the way you have done:

Transactions should protect changes to the EEPROM.

In context, this likely means that the goal is to prevent changes to the EEPROM from getting stuck halfway. A transaction essentially records the initial state of the EEPROM and, if the change gets interrupted for some reason, allows you to roll back to that initial state and try again (instead of being stuck with half-written data).