My stationary source has a process that contains a maximum of 4,000 lbs. of a regulated substance that has a 5,000 lb. threshold quantity. When the level of the regulated substance in the process reaches 1,000 lbs., a delivery truck comes on site and connects to the process to replenish the supply. The tank on the truck holds 10,000 lbs. of the regulated substance. Must I consider the amount of the regulated substance in the truck's tank to be a part of my process while the transfer hoses are connected, and therefore complete an RMP for this process?

No, the regulated substance in the truck's tank would not be considered part of your process. A regulated substance in a truck's tank is considered "in transportation," and thus not part of a source's process, as long as the tank is attached to the truck's motive power (i.e., its cab or engine). Since in your case the motive power remains attached to the tank, only the amount of regulated substance your source accepts must be counted towards the threshold quantity. Since your source will have no more than 4,000 lbs. of a regulated substance even after taking delivery, it will not exceed the threshold quantity for the substance.