How about this:
$filenames = @("E:\blergfest.csv")
foreach ($file in $filenames) {
$outfile = "$file" + ".out"
Get-Content $file | Foreach-object {
$_ -replace '\~}}|{{E', "`r`nE" `
-replace '\|\r\n', "`r`n"
} | Set-Content $outfile
}