Based on postings in de.comm.software.mozilla.mailnews (“[SM 2.46] Leerzeilen verschwinden beim Antworten”) I reported Bug 1329724 – Empty lines in email body disappear, but until now it seems nobody was able to reproduce the problem with the steps from bug report.
I did tests on mozilla.test with Server-Installations of unofficial (by FRG) en-US SeaMonkey 2.50a1 (NT 6.1; Win64; x64; rv:53.0) Gecko/20100101 Firefox/53.0 Build 20170108183322 (Default Classic Theme) on German WIN7 64bit (Re: Empty lines disappear, Rainer Bielefeld 06:08 +0100, Message-ID: <V8OdnYbIGKeq8enFnZ2dnUU7-cOdnZ2d@mozilla.org>, and the issue was still reproducible.
It would be great if someone else could reproduce the problem with the Steps To Reproduce from my report.
And, of course, it also would be great if you find other reliable ways how to provoke disappearing empty lines in replies; please submit additional separate Bugs if you are not sure that the problem you observe is exactly the same.