Dealing with hold-ups during editing

In writers' workshops, I've always found it confusing when writers offer alternative readings for a paragraph or announce that sections in their manuscript are 'to be arranged'. 

How can you comment on two versions at once? 

Now I find myself doing something similar when coming across a problematic chapter. By which I mean a section that diverts from the main plot, is intended as humour but is a bit too knowing or even irrelevant. 

I can't simply cut it out because I need a pause, a change of scene, a change of pace or I want to create tension and delay a reveal. Scenes like this arise because I have two alternating voices in two locations, one first person and the other third person, it's not a simple thing that I can fix in one session.

I'm at risk of losing steam in the three-pages-a-day edit that will see me reach the end by the end of the month. I worry that if I slow down and fix small rpoblems I'll 'loose the plot' ie miss out on the narrative trajectory.

Why don't I just fix that chapter? I need to see the manuscript as a whole. I need to get back to the narrative voice that I recognise. I'll decide later how the problem can be fixed. 
If I linger too long I run the risk of losing momentum and compounding the problem which is relatively small in comparison with the task of creative continuity witrh a consisten voice.
So what's the solution?
I've decided to change the font colour so I know that that section needs to be revised when I read through it next time. Anyone got any other suggestions?