as reflinks.py by default runs renerence deduplication it breaks existing ref groups if templates are used .
in the example below it changes existing group name from <ref name="CIAAW"> to autogenerated <ref name=wygenerowany automatycznie1>
in the result it breaks the connection to ref groups introduced by templates {{r|CIAAW}}{{u|CIAAW}}
{{r}} is connected to grouped References - english equivalent {{r})
{{u}} is connected to grouped Notes

$ python pwb.py reflinks.py -page:Azot -lang:pl
Retrieving 1 pages from wikipedia:pl.
PDF file.
Bad link : http://web.archive.org/web/20140226213530/http://cybra.lodz.pl/Content/291/ChePol+X+12.pdf in [[Azot]]

>>> Azot <<<
@@ -178 +178 @@
- * <ref name="CIAAW">{{IUPAC-SAW2013}}</ref>
+ * <ref name=wygenerowany automatycznie1>{{IUPAC-SAW2013}}</ref>

Script should not change the name of the reference if it finds one.
Or to introduce a new switch -nodedup to disalow deduplication.

More complex is to observe all reference group introducing templates but that would be to time consuming to implement