A channel is disabled if a channel_update message has been broadcast for that channel with the disable bit set (see BOLT 7). It means that the channel still exists but cannot be used to route payments, until it has been re-enabled.
Suppose you're A, with the following setup:
A ---ab--> B --bc--> C
And node C goes down. B will publish a channel update for channel bc with the disable bit set.
There are other cases when a channel becomes disabled, for example when its balance goes below reserve...
Note that you can have multiple channels between the same nodes, and that some of them can be enabled while others are disabled (i.e. enable/disable is channel-specific, not node-specific).
When channels are unilaterally closed, there is a delay before which closing transactions can be published: you must wait for this delay before you can get your funds back.
Once published, transactions will be automatically RBF-ed by eclair based on your configuration values for the eclair.on-chain-fees section.
Note that there is an upper bound on the feerate that will be used, configured by the eclair.on-chain-fees.max-closing-feerate parameter.
If the current feerate is higher than this value, your transactions will not confirm.
You should update eclair.on-chain-fees.max-closing-feerate in your eclair.conf and restart your node: your transactions will automatically be RBF-ed using the new feerate.
To stop your node you just need to kill its process, there is no API command to do this. The JVM handles the quit signal and notifies the node to perform clean-up. For example, there is a hook to cleanly free DB locks when using Postgres.