Thanks for your inquiry. I have tested the scenario using following code example and have not found any issue with output Pdf file. Please make sure that you attached the correct input document and using the latest version of Aspose.Words for .NET 14.8.0.
If you still face problem, please share your input document again along with output Pdf file which shows the undesired behavior. Please create a standalone/runnable simple application (for example a Console Application Project) that demonstrates the code you used to generate your output document.
I will investigate the issue on my side and provide you more information.
Document doc = new Document(MyDir + "Test+document+with+Comments.docx");
// Collect all comments in the document
NodeCollection comments = doc.GetChildNodes(NodeType.Comment, true);
// Remove all comments.
MemoryStream stream = new MemoryStream();
PdfSaveOptions options = new PdfSaveOptions();
options.SaveFormat = SaveFormat.Pdf;
File.WriteAllBytes(MyDir + "Out.pdf", stream.ToArray());