In order to debug this upstream, please provide a trace along with all 
information listed in
http://www.fetchmail.info/fetchmail-FAQ.html#G3

fetchmail is designed to *NOT* mark the messages as read if the local
MTA properly reports temporary failure, for instance, through SMTP codes
between 400 and 499 inclusively, such as 421 disk full or the MDA (if
you use --mda) through EX_TEMPFAIL from /usr/include/sysexits.h - this
is 75 on all machines I know. Fetchmail may report 19200 instead. SMTP
requires that servers return 4XX codes for temporary conditions such as
disk full.

IF however your MDA exits with 1 (procmail for instance is notorious for
all sorts of incapabilities in error handling), or your SMTP server
exits with a 5XX code, the fault is outside fetchmail and this bug
report then needs to be reassigned to the actual culprit (package).

IF the upstream server marks message for deletion implicitly on
retrieval, that's also not a fetchmail bug; particularly, with POP3,
fetchmail does not mark messages as deleted if it encounters temporary
errors. If the server overrides this, please complain to your ISP to
stop doing that and make their POP3 service conformant to RFC-1939.

-- 
[gutsy] fetchmail: mail is permanently LOST when root disk is full and 
retrieved through POP3
https://bugs.launchpad.net/bugs/138168
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