2492751 - Your system contains kernel instances of questionable state - SUM - sapcontrol displays instances with no features.

During a SUM upgrade, the phase PREP_PRE_CHECK/INSTANCELIST_INIT fails with below error:

1EETQ399 sapcontrol: Your system contains kernel instances of questionable state. Please use sapcontrol command GetSystemInstanceList to identify which instances come along without features. Run sapcontrol without options for documentation.
1EETQ399 Last error code set is: sapcontrol error
1EETQ204 Upgrade phase "INSTANCELIST_INIT" aborted with severe errors ("20170620095021")

The sapcontrol output for GetSystemInstanceList shows instances without features like below:

 /usr/sap/<SID>/SYS/exe/run/sapcontrol -prot NI_HTTP -host <hostname> -nr <instance-number> -function GetSystemInstanceList

GetSystemInstanceList
OK
hostname, instanceNr, httpPort, httpsPort, startPriority, features, dispstatus
<hostname>, <ins. nr>, 5<ins. nr>13, 0, 3, , GREEN

The output above shows status Green, but there are no features (No MESSAGESERVER, No ABAP, No GATEWAY, No ENQUE etc.). 

Note that the phase name (PREP_PRE_CHECK/INSTANCELIST_INIT) is not important. This anamoly can take place at any phase.

You referred to KBA 1911292 - 'sapcontrol: Your system contains kernel instances of questionable state' already but the kernel mentioned in KBA does not match.

SUM

sapcontrol, kernel, questionable state, features, instances, GetSystemInstanceList, INSTANCELIST_INIT, PREP_PRE_CHECK , KBA , BC-UPG-TLS-TLA , Upgrade tools for ABAP , Problem