I guess this is a known issue but since I have used a script that removed my postgresql-9.4-postgis-2.1, I\'m now unable to get rid of this SQL error under Debian.
Finally "solve" the issue compiling from source postgis 2.2.2 (that also requires gdal, proj4 and geos) and then issuing
CREATE EXTENSION postgis;
CREATE EXTENSION postgis_topology;
since DROP EXTENSION postgis;
tells me postgis wasn't present anymore.
And finally:
ALTER EXTENSION postgis UPDATE TO '2.2.2';
ALTER EXTENSION postgis_topology UPDATE TO '2.2.2';
Got access again to my geom data and functions from PostgreSQL 9.4. It seems that compiling from source updated correctly the variable path for postgresql and installed /usr/lib/postgresql/9.4/lib/postgis-2.2.so that wasn't present anymore (for postgis-2.1.so as well), even with (re)installing from apt-get.
Hope this will help.