gc c:FileWithEmptyLines.txt | where {$_ -ne ""} > c:FileWithNoEmptyLines.txt

(gc file.txt) | ? {$_.trim() -ne "" } | set-content file.txt

@(gc c:FileWithEmptyLines.txt) -match 'S'  | out-file c:FileWithNoEmptyLines

PS C:Users> (gc file.txt) | Foreach {$_.TrimEnd()} | where {$_ -ne ""} | Set-Content file.txt

(Get-Content c:FileWithEmptyLines.txt) |
    Foreach { $_ -Replace  "Old content", " New content" } |
    Set-Content c:FileWithEmptyLines.txt;

[IO.File]::ReadAllText("FileWithEmptyLines.txt") -replace 's+rn+', "`r`n" | Out-File "c:FileWithNoEmptyLines.txt"