Help with IPtables causing disconnection and blocking

By running iptables -F you are ‘flushing’ the rules, not affecting the default policy. In your case, it is set to ‘DROP’ which means that, now that all the rules are gone, all packets will be dropped.

You’d want to run iptables -X afterwards to reset everything else to the defaults. So

iptables -F
iptables -X

should allow everything to go through.

What errors do you get when you try to use yum with your IPTables rules enabled? Can you post the output of:

sudo iptables -L -n
sudo iptables-save

I would personally change the default policy to ALLOW then append a DROP at the end of your INPUT Chain, so for instances like what you described when you flush the rules you aren’t locked out.

I would also add a couple of rules in at the front of your INPUT Chain so your iptables-save looks like below

-A INPUT -m state --state RELATED,ESTABLISHED -j ACCEPT
-A INPUT -i lo -j ACCEPT
-A INPUT -p tcp -m tcp --dport 80 -j ACCEPT
-A INPUT -p tcp -m tcp --dport 22 -j ACCEPT
-A INPUT -j DROP