Sometimes mistakes will be made in the merging process, because Bob is human, and this may cause some of Alice's changes to be accidentally reversed. Logical edit conflicts aren't always immediately visible. Sometimes Bob may have good reasons for thinking that Alice's improvements aren't useful. In these case, Alice and Bob are expected to resolve their differences amicably.
If Alice made a small change, which Bob accidentally reversed, then Alice must not revert to her version. It is absolutely not acceptable for Alice to reverse Bob's major improvements to the page out of a desire to protect her minor improvements, or to punish Bob for his carelessness. This is particularly important if the page has subsequently been edited by, say, Sarah and Jonathan.
The best approach for Alice in this circumstance is for Alice to edit Bob's version, reinstate her minor improvements, and leave Bob's major improvements intact. She may also add something to the edit summary to indicate that she had to do this - for example: "Reinstating link which Bob accidentally removed". Bob should then apologise to Alice for his mistake, and thank her for reinstating her improvement.
If Bob repeats his error, then the best approach is for Alice to have a friendly word on his talk page, point him to this page, and ask him if he could take a little more care in the future. This is particularly important for newcomers, who may not understand the correct way to resolve edit conflicts, though even experienced users may need the occasional friendly '''reminder'''.