Could you make another attempt to upload the RPD and capture the timestamp of upload and then failure, attach below listed logs from mentioned location for the timestamp of RPD upload failure.

Log Name: bi-lcm-rest.log.0
Log Location: <Oracle_Home>/user_projects/domains/<domain name>/servers/bi_server1/logs

Log Name: bi-server1-diagnostics.log

Log Location: <Oracle_Home>/user_projects/domains/<domain name>/servers/bi_server1/logs

Can see below error messages in your attached logs:

bi-lcm-rest.log

Jun 08,2017 04:07:57 oracle.bi.lcm.rest.si.rpd.RpdEndpointV1 INFO - uploadRpd called for: ssi

Jun 08,2017 04:07:58 oracle.bi.lcm.rest.si.rpd.RpdEndpointV1 INFO - Deploying RPD file: C:\Oracle\MIDDLE~1\ORACLE~1\USER_P~1\domains\bi\config\fmwconfig\servers\bi_server1\tmp\lcmrest\temp-ssi-rpd7063087579559660294\uploaded.rpd

Jun 08,2017 04:08:41 oracle.bi.lcm.rest.si.rpd.RpdEndpointV1 SEVERE - Exception during RPD file upload: oracle.bi.server.customization.utils.CustomizationException: oracle.bi.server.customization.utils.ServerException: java.sql.SQLException: oracle.bi.ccs.client.NodeFinderException:

The Oracle BI Server is currently unavailable for queries. Please contact your System Administrator to report the failure.

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Caused by: oracle.bi.server.customization.utils.ServerException: java.sql.SQLException: oracle.bi.ccs.client.NodeFinderException:

The Oracle BI Server is currently unavailable for queries. Please contact your System Administrator to report the failure.

bi_server1-diagnostics.log

[2017-06-08T04:08:41.829-06:00] [bi_server1] [WARNING] [] [oracle.bi.jdbc.AnaJdbcConnection] [tid: pool-43-thread-6] [userId: weblogic] [ecid: 30e09427-8f52-4ae1-b114-f9573177b7e3-00020c16,0:3] [APP: bi-lcm-rest] [partition-name: DOMAIN] [tenant-name: GLOBAL] The Oracle BI Server is currently unavailable for queries. Please contact your System Administrator to report the failure.

[2017-06-08T04:08:41.834-06:00] [bi_server1] [WARNING] [] [oracle.bi.jdbc.AnaJdbcConnection] [tid: pool-43-thread-6] [userId: weblogic] [ecid: 30e09427-8f52-4ae1-b114-f9573177b7e3-00020c16,0:3] [APP: bi-lcm-rest] [partition-name: DOMAIN] [tenant-name: GLOBAL] The Oracle BI Server is currently unavailable for queries. Please contact your System Administrator to report the failure.

[2017-06-08T04:08:41.845-06:00] [bi_server1] [WARNING] [] [oracle.bi.jdbc.AnaJdbcConnection] [tid: pool-43-thread-6] [userId: weblogic] [ecid: 30e09427-8f52-4ae1-b114-f9573177b7e3-00020c16,0:3] [APP: bi-lcm-rest] [partition-name: DOMAIN] [tenant-name: GLOBAL] The Oracle BI Server is currently unavailable for queries. Please contact your System Administrator to report the failure.

Looks like there is still some problem with your OBIS1 server, could you check if your OBIS1 server is up and running?

are you able to open RPD in online mode even though its a empty RPD?

are you able to login into analytics application?

Do you see strange ODBC errors on the front end?

Have you tried shutting your service down, replacing the current rpd with the default rpd and then restarting and using your original rpd (validated in off line mode first to check it is 100% a-okay) to upload?