Você poderia tentar passar o sinalizador -m para o apt-get para tentar "ignorar pacotes perdidos", isso poderia funcionar.
Veja o arquivo man do apt-get:
-m, --ignore-missing, --fix-missing
Ignore missing packages; If packages cannot be retrieved or fail
the integrity check after retrieval (corrupted package files), hold
back those packages and handle the result. Use of this option
together with -f may produce an error in some situations. If a
package is selected for installation (particularly if it is
mentioned on the command line) and it could not be downloaded then
it will be silently held back. Configuration Item:
APT::Get::Fix-Missing.