You need a trigger module that will catch updates to your Pipedrive Deals, so yes, you still need the Watch Deals module.
It’s going to look something like this (note - I haven’t tested this scenario, so you’ll likely need to debug!):
You don’t need the Search Organizations module. That searches all Orgs in your Pipedrive instance. You already have the Organization Name available in the output fields from Watch Deals.
The router has three branches rather than two - this is because you want to do the bottom route no matter what. It continues on after either of the top two routes have completed.
The first filter compares the Org name to a null string and continues if it’s not null:
It then creates the new Folder in the Employer folder:
And then stores the ID of the folder in a variable (more on this later):

The next filter compares the Org name to a null string and continues if it is null:
Then it creates the folder in the Applicant folder:
And stores the Folder ID for this path (no image as it’s the same as before).
The last path from the router has no filter on it … it always executes. If you created the routes in this order, then this route will always execute last (you can check the order by right-clicking on the Router and selecting “Order routes”).
The very first step on this path is the Get variable module to retrieve the value of the Folder ID variable. Variable values are available only on the path they’re set on … unless you use a Get variable module to retrieve it (this is a common design pattern in Make when you have a set of steps that you want to run after some alternative routes, as in this case):
Next, you want to mimic the missing “Copy folders” functionality. First, we search for all folders within a Templates folder:
That’s going to return a series of bundles, one for each sub-folder that’s been found. The next module creates a folder with the same name in the target Applicant/Employer folder we created earlier, whose ID we retrieved:
Lastly, you want to save the Folder ID variable value in a custom field (not shown in the following image) on the Pipedrive Person record - confusingly, the Pipedrive API calls the Person ID “value” in this case:
The last thing to note is that there’s a filter before this module so that it only executes after all the sub-folders have been created, using the bundle number from the Search for Files/Folders module. Otherwise, it would run for each subfolder (and use unnecessary operations):