Mid-procedure termination of a mononuclear cell collection procedure may prevent collection of an amount of red blood cells that is required to harvest a complete mononuclear cell product. Blood separation systems and methods are provided for minimizing the impact of or recovering from mid-procedure termination of such a mononuclear cell collection procedure. According to one approach, blood or separated red blood cells are conveyed into a red blood cell collection container relatively early in the procedure to minimize the impact of a later termination of the procedure. According to another approach, blood and/or separated red blood cells within a fluid processing assembly are redirected through the fluid processing assembly following mid-procedure termination to allow for at least partial mononuclear cell collection. According to yet another approach, a double-needle fluid processing assembly may be converted into a single-needle configuration to allow for continued processing following mid-procedure termination.