I've hit this problem too. The only thing I can think of is to split the notes. At present I use a single census note with date on each line followed by source link to the relevant UK Census Source form.
It will be a slog for me working through them all Here is how one of my census notes looks like in GEDCOM 0@N6@ NOTE 1 CONC 1851 1 CONC 1961 1 CONC 1871 1 CONC 1881 1 CONC 1891 1 CONC 1901 2 SOUR @S71@ 2 SOUR @S4336@ 2 SOUR @S3566@ 2 SOUR @S3567@ 2 SOUR @S1391@ 2 SOUR @S66@ 2 SOUR @S1419@
If split into separate Notes it would be fine. To find all the relevant notes I could do a Find Anything for Census starts 18, mark everybody in the list, convert the entries and clear the mark as I went through.