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Remove the second half of your mods list; test whatever was breaking. If it works now or doesn't, you now know which half the mod's in. Now add it back in but remove half of that section to find which quarter it's in. Do again another time or two if needed. By the time you're down to 5-10 mods, you may be able to just eyeball what would be causing the issue; if not, test each individually.
If that doesn't work, turn off mods that you know affect world gen. Biomes, factions, unusual land forms, maybe things dedicated to helping you find places to start.
If all that doesn't work, then yeah you might as well try shutting them off in sections.
Disabling 10-20 at a time is more tedious, but is also more likely to narrow it down without causing more issues. If the error remains, reenable those, and disable the next 10-20. I've had to do this before. It's tedious, but it works for larger mod lists.
I have a hair under 300 and it's the method I've used several times. Always remove the bottom half first to avoid accidentally removing dependencies. If you have something that needs to be at the bottom, like Rocketman, go ahead and leave it in... Unless it's the suspect. When removing a quarter, again remove the bottom of the two. Oh, and try to keep mods and the mods that depend on them close when possible. Helps when you're attempting either your or my method.
Let's say you have 300 mods with nary a clue which mod does it. Disabling 10 at a time will take you up to 30 restarts to find the issue (well, to find which block of 10 mods is the issue). 20 at a time, 15 restarts. By halves you can get it down to one of 10 mods in 5 restarts. One of 3 mods in 7. By restart 9 you've narrowed it down to a single mod, if you haven't already found it by then.
This said, this method works well for most issues only detected in saves as well, as mods overall don't break things to an extreme degree when removing them from a save. Some mods can cause some extreme issues like black screens or saves that just won't load, but so long as you don't re-save the save, some generic issues like your modded food going poof or all compacted steel in the mountains turning into chicken meat won't affect your troubleshooting to see if removing a mod fixed an issue. All depending on the issue you were facing, of course, but in 9 cases out of 10, removing by halves is by far the most efficient troubleshooting method.
If you were doing fine until one day things broke, the faster way would be to scan the updated mods in your Workshop list. Focus on those that were updated within the past 24 hours, for example. Errors don't usually come out of nowhere from a stable and functioning list.
If you added something within those 24 hours, get rid of that first, because it's likely something broke when you added it. If there were a bunch, do the "half" method the others described; you'd be dealing with a couple of mods at most instead of 300.
In the worst case scenario I'd suggest starting afresh and loading in (instead of taking out) mods in blocks, starting with those you're fairly certain won't affect world gen. I tend not to be too attached to my saves so if they go belly up I just nuke them and take the opportunity to clean up my mod list (which hasn't happened often since I keep a fairly stable mod list).
I used to pre-1.4, but my mods list had just kind of gradually grown. Updating it after the 1.4 modpocalypse...Nope, not manually.