App Engine: Few big scripts or many small ones?
A single big script would have to be loaded every time an instance for your app starts, possibly hurting the instance start time, the response time of every request starting an instance and the memory footprint of the instance. But it can handle any request immediately, no additional code needs to be loaded.
Multiple smaller scripts can be lazy-loaded, on demand, after your app is started, offering advantages maybe appealing to some apps:

the main app/module script can be kept small, which keeps the instance startup time short
the app's memory footprint can be kept smaller, handler code in lazy-loaded files is not loaded until there are requests for such handlers - interesting for rarely used handlers
the extra delay in response time for a request which requires loading the handler code is smaller as only one smaller script needs to be loaded.

Of course, the disadvantage is that some requests will have longer than usual latencies due to loading of the handler scripts: in the worst case the number of affected requests is the number of scripts per every instance lifetime.
Updating a user profile is not something done very often, I'd consider it a rarely used piece of functionality, thus placing its handlers in a separate file looks appealing. Splitting it into one handler per file - I find that maybe a bit extreme. It's really is up to you, you know better your app and your style.
From the GAE (caching) infra perspective - the file quota is 10000 files, I wouldn't worry too much with just ~100 files.
I am working on a website that I want to host on App Engine. My App Engine scripts are written in Python. Now let's say you could register on my website and have a user profile. Now, the user Profile is kind of extensive and has more than 50 different ndb properties (just for the sake of an example).
If the user wants to edit his records (which he can to some extend) he may do so through my website send a request to the app engine backend.
The way the profile is section, often about 5 to 10 properties fall into a small subsection or container of the page. On the server side I would have multiple small scripts to handle editing small sections of the whole Profile. For example one script would update "adress information", another one would update "interests" and an "about me" text. This way I end up with 5 scripts or so. The advantage is that each script is easy to maintain and only does one specific thing. But I don't know if something like this is smart performance wise. Because if I maintain this habbit for the rest of the page I'll probably end up with about 100 or more different .py scripts and a very big app.yaml and I have no idea how efficiently they are cached on the google servers.
So tl;dr:
Are many small backend scripts to perform small tasks on my App Engine backend a good idea or should I use few scripts which can handle a whole array of different tasks?