Josh, I know, but it is back now.

Ton,
The Apply to All check box was removed in some versions.

If the linked files are missing because the original folder has been renamed or moved, and the links are in the same folder, it works when you click Replace and select a missing file in the new location. All files are found. If the missing links are in different folders, you need to repeat the locating.
The other scenario; replace multiple copies of the same missing image with a different image works fine if you check the Apply to All checkbox that appears when opening the file, click Replace and point to whatever file you want.
This is how it works on my Mac.
But I prefer the InDesign way; controlling and replacing links from the Links panel.

"Search for Missing Links in This Folder" was an option for me, and I’m on Windows 10 as well... Was exactly in the same position at InDesign has it in, in the right bottom corner of the Place dialog, next to the Place and Cancel buttons. Doesn’t matter though, it’s gone now.

As for the relinking... again, works for me.
Here is what I do to check it:
1. I create a folder '1' and put three PNGs there
2. I link all three into a document
3. I relink the folder into '2'
4. Ai throws me a warning, 'some files are missing or modified, wanna update' — I chose Yes
5. It fails to find the link and offers to Replace or Ignore — I enable 'Apply to All', click 'Replace'
6. I locate the folder in the Replace dialog opened, choose no file and just click another 'Replace'
All three images get relinked.

In case you want to replace several copies of the same image (or even different image) with another image at once...
Well, this is one of reasons this whole story with options being messed with happened in the first place.
There is a separate request for this, 'Relink / replace all instances of the same image at once' — http://illustrator.uservoice.com/forums/333657/suggestions/34174264

InDesign treats copies of the same image as duplicates.
Illustrator does not. And 'Replace All' is just a controversial name for the command in this case, and different users expect different results because of this.

Maddening, for sure!
Luckily for us, there are TWO FREE scripts we can use to avoid clicking the Replace button 154 times:
1. Fast Relink by Marat Shagiev: https://github.com/dumbm1/ai_scripts/blob/master/jsx/fast_relink.jsx
2. Relink All Selected by Carlos Canto and the community: https://community.adobe.com/t5/illustrator-discussions/relink-all-selected/td-p/9332967

These were mentioned several times in comments below.
Please use them to save time!
Running scripts is easy — you can just drag-n-drop it in the Ai window, that’s it.
At least the team is now FULLY aware of the problem and all the uses we mean to have.

lol, sorry I spoke to soon, it doesn't work like it use to, you still have to do them one by one, It will only relink the ones with the same name instead of you just clicking one missing link and it automatically adding the others. at this point they are just f*cking with us.

HOLY **** they finally added the "apply to all" option back... well for now until they remove it again. I guess they finally realized the "Search for Missing Links in This Folder" option they keep referring use to doesn't exists on all operating systems, Im on windows 10 and it was never an option.

I find this out after spending an 30mins relinking 154 images one by one that there was a new update out...

Scott you DO need to change the file names if your production environment or situation requires you to keep the initial iteration in the folder. It is easier to just quick add a letter or symbol to your file name quick than it is to make a folder, name it whatever and drag the file in. Either way you shouldn't have to do either options, it should just be a feature.

RV999-You don't need to change any file names. Any file you want Illustrator not to find can go into a seperate folder. When the original layout is opened, it will ask for the missing files.

Agree with RV999. Why doesn't this feature exist when using the Relink option? Such a silly work around you have to do just to relink a bulk amount of images.

Muchas gracias!!!

Thank you Adobe !! Now we can all move on with our lives

ok the Apply to All is back but it's still NOT an ideal workflow: the ideal is the way Indesign works: where I can click on a link in the side panel, click on relink, choose a new file and check "apply to all" if I want all the instances to be changed. Simple, InDesign has it, WHY is Illustrator so backward?

Now in Illustrator if I have a linked image used 20 times in the file, I first need to modify the link name to something else so Illustrator prompts me with the “some files are missing or modified in the Links panel. Would you like to update them now?”

Only THEN, in the next warning screen that says “Could not find the linked file ***” you can click on Replace and check the famous APPLY TO ALL tickbox.

Why is it not possible to avoid this fake-name-change in the first place?? Why is it not possible to have the InDesign behaviour/interface? Please copy your own code from your sister software, it really cannot be THIS hard??

The latest release is finally here! This function works exactly as it did before and we are all very happy to finally be able to update Illustrator. Thank you for adding this much needed function back!

This is wonderful! I tried it in the new Beta version and it works as expected!
However, I still don't see an update for the full version 29.2 yet. When is this going to be available?

Glad to see we have this function back. V29.2 is not showing up as an available download in Creative Cloud. Supposed to be released yesterday. Is there another option for uprgrading?

this is very good action thanks a lot

Version 28.4.1 has a major bullet point and type on path bug. I'm asking for Adobe create another patch for 28 to bring it back. We can't quite upgrade to 29 yet.

Josh, I don't think so, but you can install an older version of Illustrator: 2023 (28.4.1), a version that still has the Apply to All option:
In the Creative Cloud app select Apps > All Apps > Illustrator > click the 3 dots … next to the Open button > click Other Versions and select 28.4.1. Click Install.

Can we get it patched out of version 28 too?

Hurra !!
its back again. Just installed 29.2 (German).