Holmes perceived Mcdonald's case as a hopeless one and he asked them to abandon the case.

True, he did tell them to abandon the case.... but he did not tell them to abandon seeking the truth.

Therefore I am here to advise you this morning, and my advice to you is summed up in three words—abandon the case.”
MacDonald and White Mason stared in amazement at their celebrated colleague.
“You consider it hopeless!” cried the inspector.
“I consider your case to be hopeless. I do not consider that it is hopeless to arrive at the truth.”