The process has been designed to consider agile development requirements in the project where developers check-in their respective code changes (.sql files, .rdl files etc) to a particular build. The build once freezes for release, goes through various environment. This is the reason we need to copy all the relevant files to a particular location.
There is a way to stop timing out of .sql files by adding a line of code in SQL Server related PowerShell scripts.
$SQLCommand = New-Object System.Data.SqlClient.SqlCommand($SQLSTMT, $SQLConnection)
$value = $SQLCommand.ExecuteScalar()
Here, timeout value(1000) is in seconds.
Hope this will help you in your deployments.