You can implement the Expression editor class for your custom property to enable same Expression Editor functionality to delete value for custom property. find below sample for the same.

// --> Implement an Explicit Class  called  ->
            Workflow.NET.ExpressionHandler

Along with IPropertyType interface

            this.IsExpression //-> will give whether user has chosen from expression editor or not
            this.GetProcessedValue(InitializationContextObject.CurrentContext).ToString();//will compile the expression built by user.

            void IPropertyType.ReadXml( System.Xml.XmlTextReader xtr )
            {
            this._PropertyTypeforCompile = "String";//This is a property from ExpressionHandler which determines the return type.
            if(!ReadExpressionXml(xtr))//This is a builtin method from ExpressionHandler similar to read Xml/WriteXml . //Similarly we have read ExpressionXml and Write ExpressionXml.
           _value = xtr.ReadElementString();
            }
            /// <summary>
            /// Implements IPropertyType.WriteXml.
            /// </summary>         
            void IPropertyType.WriteXml( System.Xml.XmlTextWriter xtw )
            {
           
            if (!WriteExpressionXml(xtw))//Only if user doesnt select from expression editor
                xtw.WriteCData(_value);           
            }
Regards,

Anil.