If you run multiple scripts in parallel, it may happen then one script tries to read the file at the same time another one is writing it.
As a first thing, try setting the INI file read only to prevent WinSCP trying to write to it on exit.
https://winscp.net/eng/docs/config#readonly
Though in general, we do not recommend relying on configuration files:
https://winscp.net/eng/docs/scripting#configuration

Hello Team,

We are using WinSCP from last 10 years but now a days we are facing some weird issues with it. We have installed WinSCP on one of the SQL server and having more than 50 saved FTP connections on it which we are using to automate the things. Problem is we are losing the saved connection and due to that automation processes are affecting. Then always we have to restore .ini config file from backup.
FYI.. Server/OS details:-
1. Windows Server 2012 Datacenter Edition (Build 9200) (64-bit)
2. Winscp Version:- 5.7.7 (Build(6257)

Also we are using some other tools on this machine.

Kindly request you to please look in to it and provide us a solution for this.