Hi UnknownFea,
As per your description, yes if we give access permission to parent folder, the external users also get access to sub-folder within the parent. When we set the permissions on the root folder level, and it will be inherited to the two sub folders.
As you mentioned, “I've tried removing the user from the sub-folder(s) in question, but when I go to manage access for the sub-folders, the user isn't listed and I'm unable to remove or change permissions for that user.” does it means if you click Manage access>Advance and users are not listed there? if users are not listed there, that mean users don’t have access to that sub-folder. Please confirm with external users are able to see the subfolder.
Regarding to, “Is there a way to restrict which sub-folders the user has access to?” here is my steps:
1.Select the sub-folder that you don’t want to give access to external users>Manage access>Advance>select the users and click on delete unique permissions
2.Under Inheritance, click on stop inheriting permissions>then select the users>Modify>Remove User permission .
Users will not be able to see the sub-folder when they access root/parent shared folder.
See user end side, access parent folder result(users not able to see sub-folder1):
I appreciate your understanding and stay safe!!
Best Regards
Waqas Muhammad