We are having problems where the portals are not deleting when we remove. It acknowledges that we deleted through name. But the portals still remain and trying to do the remove with the name while looking at does not acknowledge that there's a bubble there. Are the bubbles loaded to memory and need a server restart to wipe?

Update: after a server restart it cleared the removed portals. However this is not sustainable long term, anyway to fix?

Thank you for reporting that. That'd likely be considered a bug, I'll look into it.
EIDT: Did you also get any errors in console or your logs when the portals weren't fully removed?

Failed to call hook 'PortalCommand' on plugin 'Portals v3.0.0' (NullReferenceException: Object reference not set to an instance of an object)
  at Oxide.Plugins.Portals+<PortalCommand>c__AnonStorey0.<>m__0 (Oxide.Plugins.Portals+Portal p) [0x00006] in <26a6ae597b52471395ed4416c681983e>:0 
  at System.Linq.Enumerable.TryGetFirst[TSource] (System.Collections.Generic.IEnumerable`1[T] source, System.Func`2[T,TResult] predicate, System.Boolean& found) [0x0003f] in <351e49e2a5bf4fd6beabb458ce2255f3>:0 
  at System.Linq.Enumerable.FirstOrDefault[TSource] (System.Collections.Generic.IEnumerable`1[T] source, System.Func`2[T,TResult] predicate) [0x00000] in <351e49e2a5bf4fd6beabb458ce2255f3>:0 
  at Oxide.Plugins.Portals.PortalCommand (BasePlayer player, System.String cmd, System.String[] args) [0x000c3] in <26a6ae597b52471395ed4416c681983e>:0 
  at Oxide.Plugins.Portals.DirectCallHook (System.String name, System.Object& ret, System.Object[] args) [0x000dd] in <26a6ae597b52471395ed4416c681983e>:0 
  at Oxide.Plugins.CSharpPlugin.InvokeMethod (Oxide.Core.Plugins.HookMethod method, System.Object[] args) [0x00079] in <3e46d2a997e94a3cb08cf065508cd483>:0 
  at Oxide.Core.Plugins.CSPlugin.OnCallHook (System.String name, System.Object[] args) [0x000d8] in <1fe782f4b27a43ae85d29ebb2d56c007>:0 
  at Oxide.Core.Plugins.Plugin.CallHook (System.String hook, System.Object[] args) [0x00060] in <1fe782f4b27a43ae85d29ebb2d56c007>:0

This should be fixed with version 3.1.0.