Short story, InDesign DOES support batching, as follow:
Open the Links window.
Two ways to handle it:
First way does a little at a time. If your first sequence of files are from one folder, the next sequence from another (e.g. chapter1, then chapter2 etc files), then select all the first folder's files by clicking the first file and then shift-click the last.
All from that folder get marked. Then click the upper right menu and select Relink to Folder.
Now navigate to the destination folder you want. It will relink all but report the number that didn't get relinked (cuz they aren't in the destination).
Repeat for each chapter.
If any are missing, find them by clicking each file and read the file path in the bottom window. Relink each.
Second approach didn't prove as convenient for me, because some files were missing in the new destination.
Similar to above, but select every file in the Links window and relink to the first destination folder. It will report a large number that aren't in that folder. It selects those for you.
Now repeat for each destination folder, till all files have been relinked.