I may have the same issue, though in my case, I'm not trying a bulk operation, just deleting a single, very large mailFolder. I get timeout errors with the SDK, though I've tried working around the SDK to no avail:
#approach 1
Invoke-WebRequest -TimeoutSec <big number>
#approach 2
Invoke-RestMethod -TimeoutSec <big number>
#approach 3
$uri = 'https://graph.microsoft.com/v1.0/users/<redacted>'
$req = [Net.HttpWebRequest]::Create($uri)
$req.Headers.Add("Authorization", "Bearer $($token.AccessToken)")
$req.Method = "DELETE"
$req.Timeout = ($req.Timeout * 10) # Default is 100000
$response = $req.GetResponse()
$req | fl
$response | fl
Are there better ways to manage/troubleshoot timeouts?