How to filter a file by name file with different extension file using PowerShell?

One approach you could take is:

• Get all files with Get-ChildItem and sort by extension in a descending manner. So this means .que will come before .pro files. We can use Sort-Object here to sort a calculated property which extracts the extension with System.IO.Path.GetExtension(), also ensuring we set Descending = $true to sort in descending order.
• Add files to a hash table, where the key is the last item from splitting the filename by "_" e.g. key will become A1 from file123_A1. The idea here to replace .que files with .pro files if found.
• Iterate the hash table and copy the latest file. If a .pro file was found, then it will be copied instead of the .que file. If no .pro file was found, then we copy the .que file instead.

Demo:

$directory = "D:\601"

# sort files by extension in descending order
$files = Get-ChildItem -Path $directory | Sort-Object -Property @{Expression = {[System.IO.Path]::GetExtension($_)}; Descending = $true}

# add files to hashtable. .que will be updated by .pro if found
$ht = @{}
foreach ($file in $files)
{
    $key = $file.BaseName.Split("_")[-1]
    $ht[$key] = $file.FullName
}

# copy files here
foreach ($entry in $ht.GetEnumerator())
{
    Copy-Item -Path $entry.Value -Destination .\
}

Which will copy the following files to your current working directory .\:

D:\file456_B2.que
D:\file890_11_C2.pro
D:\file123_00_A1.pro

Here we can see file123_A1.que was excluded from the copying, because file123_00_A1.pro replaced it.