When I do a substantive/line edit for a client, there are often a LOT of tracked changes to deal with. (A recent 50,000-word manuscript had more than 13,000 tracked changes in it.)
Here's the process I generally recommend my clients follow when getting back a heavily edited manuscript like this. I send two versions, a clean version (with all changes accepted; this version only has the comment bubbles remaining) and the marked-up version with all tracked changes still live.
1. First, read through the text of the clean version (ignoring or hiding comments) to see how the edited document flows and hangs together.
2. Read through the comments on the clean version to see the broad thrust of the queries and to get an idea of the kinds of changes I'm asking you to make.
3. Dig into the version with tracked changes:
a. First, hide formatting changes to reduce the visual clutter. (You can accept them if you want, but I often use highlighting to draw your attention to particular passages; it's easier to remove the highlighting by rejecting the change than by selecting and applying "no highlight" to the text.)
b. Next, go through and accept the changes that you are fine with. (If you select a bunch of text whose changes you want to accept and hit the “accept changes” button on the "Review" tab, it will accept all the changes in the selected text, but none outside the selected text; this keeps you from having to go change-by-change.) Leave unaccepted the changes you want to ponder.
c. Address the comments and queries, in order; delete them as they’re resolved, leaving only the sticky ones—ones you want to think more about, or that require more intensive revision, or that need additional research to resolve.
At this point, you shouldn’t have very many changes and queries left; with a less cluttered document, you can attack these sticky remaining problems one-by-one.