First, for build and buy CC, run ALL of the batch fixes. For CAS CC, run the batch fixes that reference a specific pack or situation, then update skin tones and last of all, update makeup (this one may take a very long time depending on how much makeup you have.) Note: you may want to avoid the Cats and Dogs glass hair fix if you use alpha hairs; I don't use alpha so I don't know if that messes it up. (It may also break CC eyelashes like Kijiko's?) You may also want to run each "allow CC for x occult" but be wary of any content that should be specific to a certain occult, such as CC mermaid tails. For batch fixes, Sims 4 Studio will create a backup of any files it alters but it won't do this if you decide to alter CC manually, so make sure you create a backup of your entire mods folder before editing anything. (It's a good idea to backup your mods regularly anyway, just in case. You can do this by copying the folder and pasting it somewhere else on your computer.) After each batch fix, S4S will create a pop-up that tells you what it fixed and also opens up the folder where the batch fix backups are. If you use Windows 10, you may want to right-click the Batch Fix folder and select Pin for Quick Access so it's easy to find later, if you need to. You can also do this with your Mods folder; it'll pin them into the left-side menu of every folder you open.
For the most part, I wouldn't batch fix "allow CC for random" since the game prioritizes CC when randomizing townies and there are a lot of cool CC accessories that can be really awkward if they turn up in situations where they don't look as good: overlays for hair-wraps, hair bows, and Ombres on hairstyles that they aren't compatible with, hair without hat chops shoved into hats, accessory shirts paired with something it clips through, and regular clothing that clips with other clothing can also get ugly fast. High polygon hair and clothing also shouldn't be allowed for random because they can tank performance when NPC Sims wear them. Also, if you ever wondered why there are Sims with wacky hair colors and eyebrows that don't match, it's usually because the CC hair recolors aren't geneticized correctly. You may want to try manually allowing for random or temporarily removing the rest of your mods and running a smaller batch fix with the items you absolutely want randomized. Note: if you change a piece of CC yourself, most sections have a button that says "apply to all swatches" which can, for example, let you randomize for every swatch at once rather than doing it one by one. You can also manually geneticize things or tag them correctly for color sort/hair type/category but be careful when manually changing things. If S4S could open the item and then after you change it and save, you can no longer open the item, I believe that means the file was corrupted. (Some packages S4S can't open to begin with, like presets, sliders, and as far as I know, skin tones, so those are fine. If you could open it before and now you can't, that's an issue.) Always make sure there is a backup before manually editing anything or you may have to download it again.
Now, it could be very tedious but if you don't think the batch fixes solved your problem, you can open every piece of CC to locate the culprit. This can be time-consuming but if you're organized and you have an idea (you know it's a CC hair) then it's not as bad. Note: you may want to check everything that says recolor in the name if you're getting question marks on the Sim or a body part is missing. Recolors usually require the mesh to work but most TOUs don't allow for its inclusion, just a link back to the mesh, so check your folders to see if anything like that is missing. When you open it in S4S it should also be missing the relevant body parts. Recolored hairs without a mesh may simply appear bald; just make sure it's a hair color and not an overlay hair accessory (because S4S can only load one mesh at a time, these accessories won't appear even though they're working fine. Hair recolors will appear as long as the hair mesh is available to S4S.) If you find yourself in this situation, you can search for the recolor online to download the missing mesh. You may also want to check all of the LODs on any items that appear weird, change at random, or disappear when you zoom out. (LOD0 is what you see in CAS, LOD1 is typical gameplay close-up, LOD2 and LOD3 are when you zoom out and then the most zoomed out that you can be.) Some CC can't be repaired by S4S and you may have to tell the creator what's wrong so they can fix it. Typically, if it was broken by a specific patch or pack, active creators will fix their CC so you can sometimes delete the old copy and redownload the new version. If the CC is old and unsupported, the creator is long-gone and/or unreachable, you could potentially put in a request in the request forum to see if someone else can repair it or try repairing it yourself.
If you have a TON of CC that you suspect is broken and you just want to remove it all or you're having trouble finding it with S4S, you may want to try out the Tray Importer, which works differently but could be more helpful in that situation. www.sims4studiodownload.com/tray-importer/
Edit: I forgot to add, and you may already know this, but Sims 4 Studio can't open Mods which only affect game play, whether they're packages or scripts. For example, it can't touch MCCC or More CAS Columns. You'll have to search for those types of Mods online to see if the creator has updated them, then replace the old mod with the new file.
Another edit: Once you're pretty certain that everything is up to date, fixed, and you've cleaned out any mods that you don't want or can't fix, I'd recommend merging as many files as you can to improve your load time. Don't bother merging things you'll need to update regularly or which you frequently clean out (for me I download too many new eyes and thus end up removing or getting bored with eyes a lot, so I just don't bother merging them) but for everything you're positive you want to keep, merge away! From what I can tell, you can merge up to roughly 1.5 GB in a single file before S4S has trouble adding more CC. The number of CC files doesn't matter, only the size of them. So you'll want to merge with some rhyme and reason because unless you have very little CC, you probably can't merge all of it into one file, so just try to merge down to as few as you can get, while keeping it organized in case you need to redo it later. Keep the individual files in your backup mod folder because it's harder to unmerge than it is to merge: it's easier to just copy those files, paste them into your official mods folder, remove the ones you don't want (as well as the previous merged file), and merge the remaining files again.
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