Sorry, your question makes little sense.
To give you an answer: No there's no issue in WinSCP that would make FTP server delete files successfully uploaded by WinSCP.
Do you have any reason to believe that the issue has anything to do with WinSCP? Or is this just a random question?

Used version: 5.15.9 (Build 10071)

Environment Setup:
We have hosted the Spring MVC Project (API) in the Amazon EC2 server. and we are using the WinSCP tool to publish the latest WAR file into the Amazon EC2 server for the past 3 Years.

Problem:
The past week we have encountered a wired issue in our Amazon EC2 server that All our WAR files are automatically deleted from the FTP server. so our team is working on the process of identifying the root cause of this issue.

Expected:
So we would like to know is there any issue in the WinScp tool (latest build or old build).
and also we request your guidelines to resolve this issue asap.