This seems to happen to me a lot: something I add to a later chapter requires that I retcon earlier chapters to fit the newly changed continuity. In this case, newly revised events in the final two flashback chapters (13 and 15) have just put events taking place in earlier chapters later in the timeline (Chapters 2-4) out of continuity. Specifically, the scenes involving two new villains added to Chapters 2 and 3 are now out of order, and one thread in Chapter 3 now takes place in the present rather than the past (earlier the day of the story i.e. as part of the flashback arc).
There's a bigger reason for this. The flashback chapters include a thread involving the COPCO agents starting in Chapter 7 and another which starts each flashback chapter, and both have tight plots. In its current state, the main thread is just a mess of expository dialogue interrupted by a few major events. The way the sideplots turned out made me realize that I need to give the flashback arc the tight plot it currently lacks. The mess is a carryover from Chapter 1 R4, in which the flashback arc was just a series of quick flashback scenes, each dedicated to a single reveal. But when I expanded Chapter 1 into an entire book, this no longer worked. Hence, the new plot.
It's the events of this new "earlier today" plot that are making me rewrite scenes in the earlier chapters. This is all for the better because it'll make for a stronger plot.