I have found it extremely difficult to discover data on this. I can state with certainty that a secret ballot was not used between July 16th 2014 and February 25th 2016 (except with respect to appointments & term extensions) thanks to this dataset  which I was able to analyse.
The only reported use of the secret ballot rule (which has changed to EP Rule 180a in the 2019-2024 parliament) I can find, aside from elections, nominations, and term extensions, is the use during the session on January 31st 2019, where amendments to Parliament's Rules of Procedure were approved during a secret ballot initiated by members from the EPP group (full session minutes).
I also found articles suggesting that the EU's budget for 2014-20 would be voted on in a secret ballot, however, the results of votes for this session show that this did not take place.
I am forced to conclude given lack of evidence to the contrary, that the aforementioned vote on lobbyist transparency is the only previous use of this rule.
-  Cherepnalkoski, Darko; Karpf, Andreas; Mozetič, Igor and Grčar, Miha, 2016,
Dataset of European Parliament roll-call votes and Twitter activities MEP 1.0, Slovenian language resource repository CLARIN.SI,