Back on 10/10/12, I wrote about a redraft I was working on for In Times Passed. I had set up two parallel plots, one linear and one non-linear. I felt pretty good about the changes, but I was uncertain about if the reader would be able to follow the non-linear plot line. I had chosen the non-linear scenes to match to the linear flow based on common links in dialogue, which seemed a reasonable approach to connecting the two plot lines.
You know that part of you that syncs together what you write, that manages the pull of imagery, purpose, characterization, depth of character, release of the gathering of facts? The inner coil that tightens as you develop plot and bothers you when things are not working. Well that place, that wellspring of creativity was giving me muffled bursts of dismay at that non-linear flow, unflow. Last week, just to check, I moved the pieces about and straightened out the sister plot so they both ran chronologically in line but not in the same time frame (one is set in the future). That muffled burst of dismay settled down with a contented sigh. There was no mistaking it.
I am letting it rest as I line edit and watch out for any more muffled bursts. My advice, if something in you is protesting, check it out. Make the changes called for and see if you find creative peace. You can always revert back to the original draft.