Document Updates in a folder via FTP considered Publish Points?

Hello,
We currently have a website that is deployed via IIS that we are planning to move to Azure Web Services.
This web contains a folder in the web site directory that contains files and documents for users to download. The site itself contains code that manages the files, and presents specific files to specific users.
Throughout the month, these files and document gets updated (additions as well as replacements); even though the website does not get updated.  Users use FTP to transfer files into current folder on the IIS server.
The issue we are facing:
My concern is that updating documents in this folder via FTP does not create a publish point (and considered as dynamic changes) and if the site is re-deployed or scaled, the document changes are not picked up.
Can anybody confirm that: If we use FTP to update documents in this folder, Azure Web Services will recognize this as a Publish Point?
Thank you.  Your help is very much appreciated.
PCR.

Thanks for the reply.
I confirmed that we are using Azure Websites.
We had a previous website with a similar situation where the website contained a folder with documents (pdf, doc, and xls).  Files were added into this folder periodically.  Then one day we noticed that a number of files were missing.  When
we researched the problem, we were led to believe that something on the back end moved the website to a different server, and used a previous instance of the website.
Our web development manager thought he found an article that stated that we should not keep dynamic files within the website structure.
It would be great if this is no longer the case (or that we are mistaken in our interpretation).

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