import re
rx = r"""(?m)(?:(?<=^)|(?<=~))"|"(?=$|~)|"(?=[^\n"~]+(?:~|$))"""
rx_0 = r"""(?m)(?:(?<=^)|(?<=~))"(.*?)"(?=$|~)"""
s = ("\"ID\"~\"Name\"~\"DESC\"\n"
"1~2014~13~\"DS\"~DF\"\n"
"1~2014~13~\"DS\"~\"DF\"\n"
"\"1ABCA~B C\"~\"ERTE\"\n"
"\"2\"~\"XYZ\"~\"ABC~ is~ bother\"\n"
"\"3\"~\"YYZ\"~\"MEL O CRÈME DOUGHNUTS RECLASS\"\n"
"4~\"XAA\"~\"sf~sd sdfsf\"\n"
"5~\"TES\"~\"SFSFSF\"sdfsf\"\n"
"6~\"ABC\"SDDSL~\"dfadf\"")
print( re.sub(rx, "", re.sub(rx_0, lambda x: x.group(1).replace('~', ' '), s)))
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