Fanfiction.net doesn't support certain characters after dot(full stop), therefore if you have letters after dot, in some cases letters will be missing.
This happened to me when I uploaded my first fanfiction on fanfiction.net.
You will need to put a space after dot, so the letters will remain.
For example, if you write a disclaimer, saying that the universe belongs to J.K.Rowling, letters will be missed, therefore use J.K. Rowing instead, this will preserve the letters, put a space after the second dot.
I made my account in Fanfiction website.I made a Fanfiction in Microsoft Word 2010 and I saved in the website.I made a Fanfiction,and I've wait 4 hours.When I read,letters were missing!What happened?!