Yes, I have the index entries but I don't have index values attached as 
properties (but the index values are formed/merged solely out of the node 
properties).

Could share the db, no sensitive information there, but I think we have 
just reached the point when it's gonna be easier/cleaner if I just rollback 
to the latest backup and reapply the commits of several missing days.

Another thing. I was trying to find any sign of the "unclean shutdown", but 
I do not really see this.. For instance, in the console.log I see:

2014-03-04 18:01:55.296+0000 INFO [API] Neo4j Server shutdown initiated by 
request

2014-03-04 22:43:32.800+0000 INFO [API] Setting startup timeout to: 
120000ms based on -1

2014-03-04 22:43:35.848+0000 INFO [API] Successfully started database

2014-03-04 22:43:35.881+0000 INFO [API] Starting HTTP on port :7474 with 
240 threads available

2014-03-04 22:43:36.142+0000 INFO [API] Enabling HTTPS on port :7473

2014-03-04 22:43:36.895+0000 INFO [API] Mounted REST API at: /db/manage/

2014-03-04 22:43:36.897+0000 INFO [API] Mounted discovery module at [/]

2014-03-04 22:43:36.935+0000 INFO [API] Loaded server plugin "CypherPlugin"

2014-03-04 22:43:36.938+0000 INFO [API] Loaded server plugin "GremlinPlugin"

2014-03-04 22:43:36.940+0000 INFO [API] Mounted REST API at [/db/data/]

2014-03-04 22:43:36.942+0000 INFO [API] Mounted management API at 
[/db/manage/]

2014-03-04 22:43:37.063+0000 INFO [API] Mounted webadmin at [/webadmin]

2014-03-04 22:43:37.150+0000 INFO [API] Mounting static content at 
[/webadmin] from [webadmin-html]

2014-03-04 22:43:38.626+0000 INFO [API] Remote interface ready and 
available at [http://localhost:7474/]

2014-03-04 22:47:18.536+0000 INFO [API] Available console sessions: SHELL: 
class org.neo4j.server.webadmin.console.ShellSessionCreator

and in the messages.log:

2014-03-04 18:01:55.589+0000 INFO [o.n.k.EmbeddedGraphDatabase]: Shutdown 
started

2014-03-04 18:01:55.599+0000 INFO [o.n.k.EmbeddedGraphDatabase]: Stopping - 
database is now unavailable

2014-03-04 18:01:55.600+0000 INFO [o.n.k.EmbeddedGraphDatabase]: GC Monitor 
stopped.

2014-03-04 18:01:55.882+0000 INFO [o.n.k.i.t.x.XaLogicalLog]: Closed log 
data/graph.db/index/lucene.log

2014-03-04 18:01:55.968+0000 INFO [o.n.k.i.t.TxManager]: TM shutting down

2014-03-04 18:01:56.187+0000 INFO [o.n.k.i.t.x.XaLogicalLog]: Closed log 
data/graph.db/nioneo_logical.log

2014-03-04 18:01:56.391+0000 INFO [o.n.k.i.n.s.StoreFactory]: 
data/graph.db/neostore.relationshiptypestore.db.names hit=0 miss=4 
switches=0 ooe=0

2014-03-04 18:01:56.511+0000 INFO [o.n.k.i.n.s.StoreFactory]: 
data/graph.db/neostore.relationshiptypestore.db hit=0 miss=2 switches=0 
ooe=0

2014-03-04 18:01:56.612+0000 INFO [o.n.k.i.n.s.StoreFactory]: 
data/graph.db/neostore.propertystore.db.strings hit=0 miss=0 switches=0 
ooe=0

2014-03-04 18:01:56.688+0000 INFO [o.n.k.i.n.s.StoreFactory]: 
data/graph.db/neostore.propertystore.db.index.keys hit=0 miss=10 switches=0 
ooe=0

2014-03-04 18:01:56.797+0000 INFO [o.n.k.i.n.s.StoreFactory]: 
data/graph.db/neostore.propertystore.db.index hit=0 miss=5 switches=0 ooe=0

2014-03-04 18:01:56.911+0000 INFO [o.n.k.i.n.s.StoreFactory]: 
data/graph.db/neostore.propertystore.db.arrays hit=0 miss=0 switches=0 ooe=0

2014-03-04 22:43:33.506+0000 INFO [o.n.k.i.DiagnosticsManager]: --- 
INITIALIZED diagnostics START ---

(........ and so on with normal startup going further..)


Seems that nothing was going terribly wrong, was it?

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