Lost root when phone rebooted - can't get to download mode only Android system recovery
On the Samsung Galaxy S4 (GT-i9505) Volume Up, Power and Home is to enter recovery mode. Volume down, Power and Home is to enter 'Download Mode'. From download mode you can make the device visible to odin. From Odin you can flash a custom recovery, or root the device with CF Auto Root and other methods such as flashing a pre-rooted stock ROM for example. 

If your device shows as not being rooted, when previously it was and you have not unrooted it manually, this could be an issue with the SuperSU binaries, and sometimes installing these via the app, or via the 'recovery' option within the app can fail. You can download the SuperSU zip from Chainfire and flash it in a custom recovery. 

Generally the safest bet is to backup anything you need, flash the Stock ROM through Odin, and root, or flash a pre-rooted stock ROM. Then you can flash a custom recovery and from that recovery flash whatever you need.