Of course the story still continues! In October 2019 the EMA posted:--

Update: In October 2019, EMA's Management Board endorsed the six-monthly monitoring report on the development of the CTIS, which assesses the performance of the IT supplier against agreed key performance indicators. The Board agreed that actions proposed in the report should be further developed, for example improving the quality of the work delivered by the supplier and selecting the critical items needed for audit, as well as extending the monitoring period for at least three releases.
The product owners validated the first release developed in the agile, iterative delivery in September 2019, confirming that all 79 items had been delivered.
The release enhanced CTIS functionalities for the submission of clinical trials and the assessment process, user management and included other general improvements.
The product owners will begin to carry out an operational assessment of the system to identify critical business blockers, in order to enable EMA's Management Board to consider the timing of the audit of the system.