I'm experiencing the same issue.
I followed these instructions but on an Ubuntu 18.04 to migrate the store from 3.5.14 to 4.0.3. I've effectively copied the contents of 3.5.14 data folder to data foldedr of 4.0.3. Migration went well according to logs. However, startup is failing.
Directories in use:
home: /var/lib/neo4j
config: /etc/neo4j
logs: /var/log/neo4j
plugins: /var/lib/neo4j/plugins
import: /var/lib/neo4j/import
data: /var/lib/neo4j/data
certificates: /var/lib/neo4j/certificates
run: /var/run/neo4j
Starting Neo4j.
2020-04-06 08:24:50.957+0000 INFO ======== Neo4j 4.0.3 ========
2020-04-06 08:24:50.964+0000 INFO Starting...
2020-04-06 08:25:05.423+0000 ERROR Failed to start Neo4j: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabaseService@2673ba1f' was successfully initialized, but failed to start. Please see the attached cause exception "Mismatching store id. Store StoreId: StoreId{creationTime=1586155486029, randomId=8142000683778803301, storeVersion=3471765337752883975, upgradeTime=1586155486029, upgradeTxId=1}. Transaction log StoreId: StoreId{creationTime=1586155296154, randomId=-806197780697231748, storeVersion=3471765337752883975, upgradeTime=1586155296154, upgradeTxId=1}". Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabaseService@2673ba1f' was successfully initialized, but failed to start. Please see the attached cause exception "Mismatching store id. Store StoreId: StoreId{creationTime=1586155486029, randomId=8142000683778803301, storeVersion=3471765337752883975, upgradeTime=1586155486029, upgradeTxId=1}. Transaction log StoreId: StoreId{creationTime=1586155296154, randomId=-806197780697231748, storeVersion=3471765337752883975, upgradeTime=1586155296154, upgradeTxId=1}".
org.neo4j.server.ServerStartupException: Starting Neo4j failed: Component 'org.neo4j.server.database.LifecycleManagingDatabaseService@2673ba1f' was successfully initialized, but failed to start. Please see the attached cause exception "Mismatching store id. Store StoreId: StoreId{creationTime=1586155486029, randomId=8142000683778803301, storeVersion=3471765337752883975, upgradeTime=1586155486029, upgradeTxId=1}. Transaction log StoreId: StoreId{creationTime=1586155296154, randomId=-806197780697231748, storeVersion=3471765337752883975, upgradeTime=1586155296154, upgradeTxId=1}".
at org.neo4j.server.exception.ServerStartupErrors.translateToServerStartupError(ServerStartupErrors.java:45)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:164)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:114)
at org.neo4j.server.ServerBootstrapper.start(ServerBootstrapper.java:89)
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:35)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.server.database.LifecycleManagingDatabaseService@2673ba1f' was successfully initialized, but failed to start. Please see the attached cause exception "Mismatching store id. Store StoreId: StoreId{creationTime=1586155486029, randomId=8142000683778803301, storeVersion=3471765337752883975, upgradeTime=1586155486029, upgradeTxId=1}. Transaction log StoreId: StoreId{creationTime=1586155296154, randomId=-806197780697231748, storeVersion=3471765337752883975, upgradeTime=1586155296154, upgradeTxId=1}".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:465)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.server.AbstractNeoServer.start(AbstractNeoServer.java:157)
... 3 more
Caused by: java.lang.RuntimeException: Error starting database server at /var/lib/neo4j/data/databases
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:167)
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.build(DatabaseManagementServiceFactory.java:145)
at org.neo4j.server.database.CommunityGraphFactory.newDatabaseManagementService(CommunityGraphFactory.java:36)
at org.neo4j.server.database.LifecycleManagingDatabaseService.start(LifecycleManagingDatabaseService.java:88)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:444)
... 5 more
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.dbms.database.DefaultSystemGraphInitializer@769a58e5' was successfully initialized, but failed to start. Please see the attached cause exception "Mismatching store id. Store StoreId: StoreId{creationTime=1586155486029, randomId=8142000683778803301, storeVersion=3471765337752883975, upgradeTime=1586155486029, upgradeTxId=1}. Transaction log StoreId: StoreId{creationTime=1586155296154, randomId=-806197780697231748, storeVersion=3471765337752883975, upgradeTime=1586155296154, upgradeTxId=1}".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:465)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:111)
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:158)
... 9 more
Caused by: org.neo4j.graphdb.DatabaseShutdownException: This database is shutdown.
at org.neo4j.kernel.availability.DatabaseAvailabilityGuard.assertDatabaseAvailable(DatabaseAvailabilityGuard.java:172)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginKernelTransaction(GraphDatabaseFacade.java:185)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransactionInternal(GraphDatabaseFacade.java:165)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:119)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:113)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTransaction(GraphDatabaseFacade.java:101)
at org.neo4j.kernel.impl.factory.GraphDatabaseFacade.beginTx(GraphDatabaseFacade.java:96)
at org.neo4j.dbms.database.DefaultSystemGraphInitializer.isSystemGraphEmpty(DefaultSystemGraphInitializer.java:100)
at org.neo4j.dbms.database.DefaultSystemGraphInitializer.initializeSystemGraph(DefaultSystemGraphInitializer.java:76)
at org.neo4j.dbms.database.DefaultSystemGraphInitializer.initializeSystemGraph(DefaultSystemGraphInitializer.java:69)
at org.neo4j.dbms.database.SystemGraphInitializer.start(SystemGraphInitializer.java:30)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.start(LifeSupport.java:444)
... 11 more
Caused by: java.lang.RuntimeException: Mismatching store id. Store StoreId: StoreId{creationTime=1586155486029, randomId=8142000683778803301, storeVersion=3471765337752883975, upgradeTime=1586155486029, upgradeTxId=1}. Transaction log StoreId: StoreId{creationTime=1586155296154, randomId=-806197780697231748, storeVersion=3471765337752883975, upgradeTime=1586155296154, upgradeTxId=1}
at org.neo4j.kernel.recovery.Recovery.validateStoreId(Recovery.java:386)
at org.neo4j.kernel.database.Database.start(Database.java:377)
at org.neo4j.dbms.database.AbstractDatabaseManager.startDatabase(AbstractDatabaseManager.java:187)
at org.neo4j.dbms.database.DefaultDatabaseManager.startDatabase(DefaultDatabaseManager.java:132)
at org.neo4j.dbms.database.DefaultDatabaseManager.startDatabase(DefaultDatabaseManager.java:36)
at org.neo4j.dbms.database.AbstractDatabaseManager.forEachDatabase(AbstractDatabaseManager.java:165)
at org.neo4j.dbms.database.AbstractDatabaseManager.startAllDatabases(AbstractDatabaseManager.java:112)
at org.neo4j.dbms.database.AbstractDatabaseManager.start(AbstractDatabaseManager.java:106)
... 12 more
2020-04-06 08:25:05.431+0000 INFO Neo4j Server shutdown initiated by request