The notes.ini parameter was added in 11.0.1FP2 (SPR# BSPRBSSPWH) to suppress output of Replication Currency alerts for specific databases that were intentionally marked as “replication disabled”. 

I used it in my environment for all databases in DominoDataDir/traveler/map. After upgrading to FP3 a couple of days ago, this parameter seemed not to work any longer. On the console I saw the following output

[2D58:0005-2910] ReplCurrency Source="traveler\map\custom\MapDir.nsf", Dest=CN=serv02/O=singultus (Q:0) traveler\map\custom\MapDir.nsf, UpdateToRepl2="03.04.2021 01:01:06", LastRepl="02.04.2020 04:01:25", TimeDiff= 16167 min, TimeDiff2=543026 min Warning="5000+ mins on replication."
 [2D58:0005-2910] ReplCurrency Source="traveler\map\iNotesPMap.nsf", Dest=CN=serv02/O=singultus (Q:1) traveler\map\iNotesPMap.nsf, UpdateToRepl2="10.04.2021 01:00:27", LastRepl="01.04.2020 15:26:41", TimeDiff= 6087 min, TimeDiff2=543781 min Warning="5000+ mins on replication."
 [2D58:0005-2910] ReplCurrency Source="traveler\map\JournalEntryMap.nsf", Dest=CN=serv02/O=singultus (Q:3) traveler\map\JournalEntryMap.nsf, UpdateToRepl2="10.04.2021 01:00:38", LastRepl="01.04.2020 15:26:41", TimeDiff= 6087 min, TimeDiff2=543781 min Warning="5000+ mins on replication."
 [2D58:0005-2910] ReplCurrency Source="traveler\map\MemoMap.nsf", Dest=CN=serv02/O=singultus (Q:3) traveler\map\MemoMap.nsf, UpdateToRepl2="10.04.2021 01:00:45", LastRepl="01.04.2020 15:26:41", TimeDiff= 6087 min, TimeDiff2=543781 min Warning="5000+ mins on replication."
 [2D58:0005-2910] ReplCurrency Source="traveler\map\PersonMap.nsf", Dest=CN=serv02/O=singultus (Q:1) traveler\map\PersonMap.nsf, UpdateToRepl2="10.04.2021 01:00:51", LastRepl="01.04.2020 15:26:41", TimeDiff= 6087 min, TimeDiff2=543781 min Warning="5000+ mins on replication."
 [2D58:0005-2910] ReplCurrency Source="traveler\map\R6JournalEntryMap.nsf", Dest=CN=serv02/O=singultus (Q:2) traveler\map\R6JournalEntryMap.nsf, UpdateToRepl2="03.04.2021 01:01:20", LastRepl="02.04.2020 04:01:51", TimeDiff= 16166 min, TimeDiff2=543026 min Warning="5000+ mins on replication."
 [2D58:0005-2910] ReplCurrency Source="traveler\map\R6PersonMap.nsf", Dest=CN=serv02/O=singultus (Q:1) traveler\map\R6PersonMap.nsf, UpdateToRepl2="10.04.2021 01:00:57", LastRepl="01.04.2020 15:26:42", TimeDiff= 6087 min, TimeDiff2=543781 min Warning="5000+ mins on replication."

I opened a support case with HCL. Here is the answer

“In FP2 there was a bug where it excluded all except the first entry in the INI. The notes.ini does not allow directories to be listed, only databases. In your case, it appeared to work in FP2 because it blocked all databases except for “traveler/map” which is not a database. So, it blocked all databases from currency checks.
And, this is now fixed in 1101FP3 (SPR # BSPRBY9RPA).“

The upcoming FP4 and V12 will not list replication disabled databases in the currency alerts (so no notes.ini is required to exclude databases disabled for replication). The notes.ini is still in FP4 and V12, but the need to exclude replication disabled databases is no longer necessary.

So, here, you need to add individual NSF names as comma separated list of dbs in the INI entry to exclude them from the replication currency check.