Missing Links when exporting to HTML file

[Ananstracated]

When exporting folders/links from bookmark manager to HTML file for backup, I have found that importing the file back into the bookmarks, there are missing URLs. 

Synopsis:  

Example (steps)

1. open bookmark manager to check for Total HTTP links 
2. enter Bookmark manager search query  as  http 
3. Selection of all links in results = 3100 
4. Export Bookmarks to HTML file. 
5. Clear all bookmarks(clean slate)
6. IN Bookmark Manager—import previously exported HTML File 
7. Repeat # 2  search query above
8. Select all links = 1200

As you see,  links out DO NOT EQUAL links in.  

However,  I have done this before, and they matched after exporting/importing html file

Also, I have seen, the export vary in cases, after I exported the file, like perhaps the bookmark manager had some kind of lock or it was processing them or maybe the Sync was interfering.  keep in mind, I did do a sort of the links and may have moved stuff around, and then decide to export.  

The questions are, how should someone wait to make sure all the changes have been processed and the file is not being changed while exporting?  

or Are there characters that throw off the bookmark manager when it comes to exporting to HTML?