Hello irler,
In cypher-shell or Neo4j Browser for your instance, how many databases are shown when you enter:
:USE system
SHOW DATABASES;
Do the names of the databases correspond to the folders you have in the databases and transactions folders? If not, then you should remove any folders that are not shown by SHOW DATABASES as they are not known by the system database.
Is there any chance that you could create the database without the name graph.db (no periods in the name), load it, stop it, dump it, and the try loading it again with a different name? Note that after the load, you still need to create it. For example:
:USE system
CREATE DATABASE xxx;
:USE xxx
<load the database (not sure how you are loading it, with Cypher?>
:USE system
STOP DATABASE xxx;
....
load database with neo4j-admin using a different database name yyy
CREATE DATABASE yyy;
:USE yyy