Preface: There's a lot of background story here. Most of it is just for fun but there are definitely clues sprinkled throughout. If you want the strict puzzle, skip on down to the bottom.
For many decades, the pastry shop on Lamuella had been run by a kindly gentleman. He had taken over the sandwich shop when the previous owner bought The King's ship and left. His younger years had seen him as a brave sailor captured by pirates who grew to conquer their ranks. The life was not what he sought and did not bring him happiness so he left the first mate in charge and wandered into the port of Laumuella. The scents drifting from the sandwich shop drew him in and he was hooked ever since. When the owner took off, the ex-pirate stepped in and turned it into a bakery. He had always loved baking, but never could as a pirate lord because the lads would surely not respect such a leader. That was many, many years ago.
The locals loved the now quite elderly man. His shop was always rich in scents and cheap in cents. It was not a life that made the baker wealthy but he felt as though his life had been rich. He married young but his bride died during childbirth, leaving him a son to raise. His son was strong and would help in the kitchen. The man never remarried but he felt his family was complete. Children would stop in on the way home from school and sneak bites of the sweets on the counter as soon as the proprietor would turn his back. Of course, they never wondered why the sweets were always fresh-out-of-the-oven warm or why the old man never seemed to turn around to discover the stolen treats until after the door jangled open at their departure. The old man was happy.
One day, anxiety broke this idyllic life. The old man was carrying out the day's ration of treats to be swiped by the kids when a sharp pain seized his chest and stole his breath. He dropped the tray, clutched at his chest, and fell to the floor, knocking over a chair on the way down. The children discovered him and ran into the street screaming for someone to help.
The man woke up in a hospital bed and saw the face of his son leaning over him. "Oh, Archie!" the old man started. "Hush, father" replied his son with a concerned look on his face. The old man worked to prop himself up better on the pillows, eventually allowing his son to help. He began again, "No, Archie, I must tell you something important. I have a secret I've kept all these years. It's not safe to tell you here but you must know!" The man stopped, his breath caught and he coughed. His soon stood to get a glass of water but the father grabbed his arm and pulled him back down with uncharacteristic strength. "Listen!" he hissed. "I haven't much time. I can feel the end coming. You must listen NOW! Under the bread kiln, there is a brick that's darker red than the rest. Pull it out and find the small metal tin behind it. There's a steel plate inside with a code inscribed on it. You must decipher that code. You know me best; only you can do this!"
The old man's grasp on his son's sleeve slackened. Wheezing, he fell back against the pillows. His breath was shallow but still he spoke. Archie leaned in to hear his father's dying ramblings: "Favorite... Cherry times... Flagged down... Apple, blueberry, chocolate... Multiply...".
The son leaned back, sure that his father was gone. He slumped back into his own chair distraught and wracked with grief. He wasn't sure if he could keep the bakery running by himself or if he even wanted to. His father was a fixture in the community and it wouldn't be the same without him. With all the grief and confusion, he almost forgot his father's words.
As he was sitting in the darkened kitchen days later and wondering how he was going to move on, Archie remembered his father's instructions. Shuffling over to the kiln, he found the brick that was indeed a darker red. All these years working the kiln and he'd never noticed. He toed it with his boot and felt it give. Bending down, he slowly pulled the brick out and stuck his hand into the darkened recess. His fingers found something hard and cool to the touch. Getting excited now, Archie extracted the tin and set it on the ground before him. Trembling, he opened the creaking lid to reveal the engraved plate inside.
3:6::0:1:::9:6::2:8:::6:8::3:6:::9:6::9:6:::9:6::0:1:::6:8::2:8 9:6::2:8:::5:4::2:8:::9:6::9:6:::6:8::9:6:::5:4::9:6:::5:4::7:4 6:8::3:6:::9:6::9:6:::5:4::0:1:::9:6::2:8:::5:4::2:8:::6:8::3:6 9:6::9:6:::4:4::7:4:::6:8::3:6:::9:6::2:8:::9:6::2:8:::5:4::2:8 9:6::9:6:::4:4::9:6:::9:6::2:8:::5:4::9:6:::5:4::0:1:::4:4::7:4
His eyes played over the markings and, with a twinkle of recognition, he began scratching out letters on some parchment. When he finished, he simply sat staring at the results for several minutes. Why had his father never shared these words with him when he was still alive? The world must know. Archie shall tell them!
What was the encoded message that the old pie maker had left his son?
This has already been answered but, for the sake of completion and future readers, here are all the clues hidden in the text. Don't read them if you want to ponder it yourself as they take you halfway to the solution.
The title describes a "Pie-Maker" but the text only ever calls him a baker.
The baker was a sailor and a pirate.
The son's name is "Archie" which is a nickname version of Archimedes who introduced a new method to approximate pi.
The dying words "Cherry times" and "Apple, Blueberry, Chocolate... Multiply" both speak to multiplying by types of pies.
The dying words "Flagged down" refers to the flags used in semaphores.