There is a web application which is in production mode for 3 years or so by now. Historically, because of different reasons there was made a decision to use database-per customer installation.

Now we came across the fact that now deployments are very slow.

Should we ever consider moving all the databases back to single one to reduce environment complexity? Or is it too risky idea?

The problem I see now is that it's very hard to merge these databases with saving referential integrity(primary keys of different database' tables can not be obviously differentiated).

Databases are not that much big, so we don't have much benefits of reduced load by having multiple databases.