If you rerun your abyss-pe command with the full name of the deleted contigs file as the last argument, it will do whatever is necessary to rebuild the file, i.e.

$ abyss-pe <... your abyss-pe params for assembly ...> myassembly-contigs.fa

or

$ abyss-pe <... your abyss-pe params for assembly ...> contigs

Replace "myassembly" in the first command with whatever the prefix is for your assembly files.

That's the beauty of 'make'. It will only run the commands that are necessary to build the target you specify. Btw, it is always wise to run abyss-pe with the --dry-run option first, to see what it would do before actually running it, i.e.

$ abyss-pe <... your abyss-pe params for assembly ...> myassembly-contigs.fa --dry-run

Btw, myassembly-contigs.fa is just a symlink to myassembly-6.fa. So if you still have myassembly-6.fa, you can recreate myassembly-contigs.fa with:

$ ln -s myassembly-6.fa myassembly-contigs.fa