The issue is that in your new session the namespace of package bit64 (where class "integer64" is defined) is not loaded, and therefore you have no access to S3 methods for class "integer64". To obtain access, you can load the namespace directly:

loadNamespace("bit64")

or you can cause the namespace to be loaded by calling any of its methods explicitly, e.g.

bit64::as.integer64(data)

(But loading or attaching package data.table will not be sufficient.)