Yes, time flies. Mostly it files in manuscripts when the rewrites are done and things get moved around, like scenes and such. Or worst, when the novice insists on editing while in the midst of writing the first draft.
The best way to write a novel is straight through, beginning to end. Never, ever go back and read more than the last paragraph before starting to write each time. Please don't jump around in the ms making changes. It is a habit worst than nail biting to break, but to move from novice to professional writer, it must be broken.
I have a friend who is one of the most stubborn women I've ever met. Honestly, when I read her ms I can tell that she has jumped back and forth while writing the first draft. Not only are there gaps and time flying involved, the tone of the characters zig-zag until I'm certain they must be schizophrenic with the number of mood changes occurring.
It is a bear to fix the time changes and gaps. One way that works (and is a lot of work) is to go through and read the ms in a printed copy - away from the computer and temptation to change other things. Write it in the margin every time change, (Friday, Tuesday, two weeks later, morning or afternoon ...something very clear). It usually means an extra read-through because it is hard to focus on too many things to check at once. But if beta readers are making notes that say, "What day is it?" then it must be done. You can bet that an agent or their reader will catch it and it might be the final blow to getting a contract offered.
That is the easy part compared to sorting out an unintentional moodiness in characters that comes from jumping around while editing or writing the first draft. I've know some who write scenes; keeping them in their own documents then stringing the scenes together with bridges. That equates to the biggest mess I've ever seen. I won't read those mss, it is just not a good way to create a storyline for fiction.
Seriously, only work on your ms from beginning to end. Regardless of whether you are writing the first draft or in the rewrite process, never jump around in the middle. Your readers might not be able to put their finger on what it is that isn't quite right, but people in the industry will see it right off.
The only way I know to fix a mixed up moody character, when that wasn't the plan and really doesn't work even if it was, is to get help. You're either going to have to hire a professional content editor or owe your best friend something very special.
Print two copies of your ms. Get your friend and some snacks and settle in for a long weekend of serious work. Don't think you can pawn it off on your friend, you have to be involved or shell out the big bucks for a pro. Read the ms aloud, but not so fast that it isn't being heard by either of you. The friend's job is to notice, if you don't, when characters are out of character. Then you have to decide if it adds to the story or is simply sloppy writing. Be honest. If a character is talking in a way that they should develop into later (you jumped around), then it has to be fixed. If a character knows something they shouldn't know yet (you jumped around), then it has to be fixed.
I know some people think it is okay to bank scenes for later and write to them. Fine, but know this: very few writers can pull that off and the tone (your voice as the writer) will show as it change from one scene to another with the "bridges" between, especially if the scenes were written out of sequence.
I bet after this, no one will write out of sequence again. That is my hope anyway.