Regex string replacement ends too soon in PowerShell

I am using PowerShell (5.1) and am trying to encode a string before I pass it in the URL, to a REST API. The API users certain characters (e.g. a colon (:) means "equal") when used between a property and its value. If a colon (for example) appears in the value portion, then it should be replaced with the URL-safe encoding (%3A).

The following PowerShell works when the string is filter=username:"user1@domain.com". The @ symbol is replaced with %40. However, if the string is, filter=username:"user1@domain.com"|"user2@domain.com", then only the first @ is replaced.

The PowerShell snipet looks like this:

$Filter = 'filter=username:"user1@domain.com"'
$pattern1 = '[^a-zA-Z\d\s]' # Match any non-alpha numeric or white space character.
$pattern2 = '(?:>:|<:|:|>|<|!:|:|~|!~|@)(?:")(.*?)(?:")' # Allow us to replace characters in the filter. We will leave some of the characters alone, since they are used by the API in certain spots. For example, ":" means equal between the property name and value but should be replaced in the value portion of the pair.
$regex = [Regex]::new($pattern2)
$regex.Matches($Filter) | ForEach-Object {
    $Filter = $Filter -replace ([regex]::Escape($_.Groups[1].value)), ([uri]::EscapeDataString($_.Groups[1].value))
}

What am I missing here?

<!-- language-all: sh -->

I'm unclear on the exact requirements, but perhaps the following does what you want:

# Sample string to transform.
$filter = 'filter=username:"user1@domain.com"|"user2@domain.com"' 

[regex]::Replace(
  $filter,
  '(?<=[:|><~@]").*?(?=")',
  {
    param($m)
    [Uri]::EscapeDataString($m.Value)
  }
)

This relies on all property values being enclosed in "..." (and having no escaped embedded ") and being preceded by any one of the following chars.: : | < > ~ @

Result (only the property values inside "..." substrings were URI-escaped):

filter=username:"user1%40domain.com"|"user2%40domain.com"

For an explanation of the regex and the ability to experiment with it, see this regex101.com page.

As for what you tried:

The only thing missing from your regex is a \| segment so as to also match a verbatim | before a property value's opening " (inserted before |@):

(?:>:|<:|:|>|<|!:|:|~|!~|\||@)(?:")(.*?)(?:")

See this regex101.com page.

However, note that your regex can be simplified, by using character sets ([...]) and removing redundant parts:

(?:[:|><~@](?:")(.*?)(?:")

This simplified form is used in the solution above, albeit via using lookaround assertions so that no capture group is necessary.