In user tracking, all host names and IP addresses went away (6000+ devices). Thinking it was an issue with my device discovery (switches, in particular) I deleted all of the switches (thinking) that it would rediscover them. After several discoveries, the switches have not come back. What can I do to resolve these issues?
This tells me that you're using two CDP seed devices, .13 and .15. You've configured a hop count of 2, so this means that these seed devices plus all devices that are at most two hops away will be discovered (and no further). So, make sure that all the devices you want to discover are within two CDP hops of these two seed devices. If you need to go further, increase or remove the hop count.
Also, you're using one SNMP community string for all devices. Make sure this is the correct community string. Even though you've configured default credentials, Discovery will only use the one community string you've configured in its SNMP Settings screen.