try this

data/defaults/crossref.yaml

@@ -7,5 +7,7 @@ filters:
     path: doi-batch-id.lua
   - type: lua
     path: flatten-references.lua
+  - type: lua
+    path: conditional-archives.lua
 
 template: '${.}/../templates/neurolibre.crossref'

data/filters/conditional-archives.lua

@@ -0,0 +1,22 @@
+function Meta(meta)
+    -- Check if each DOI is present and not set to 'N/A'
+    if meta.repository_doi and meta.repository_doi ~= 'N/A' then
+      meta.include_repository_doi = true
+    end
+    if meta.data_doi and meta.data_doi ~= 'N/A' then
+      meta.include_data_doi = true
+    end
+    if meta.book_doi and meta.book_doi ~= 'N/A' then
+      meta.include_book_doi = true
+    end
+    if meta.docker_doi and meta.docker_doi ~= 'N/A' then
+      meta.include_docker_doi = true
+    end
+    if meta.software_review_url and meta.software_review_url ~= 'N/A' then
+      meta.include_software_review = true
+    end
+    if meta.book_exec_url and meta.book_exec_url ~= 'N/A' then
+      meta.include_book_exec = true
+    end
+    return meta
+end

data/templates/neurolibre.crossref

@@ -62,14 +62,24 @@ $endfor$
           <ai:license_ref applies_to="tdm">http://creativecommons.org/licenses/by/4.0/</ai:license_ref>
         </ai:program>
         <rel:program>
-          $if(repository_doi != 'N/A')$
+          $if(include_repository_doi)$
           <rel:related_item><rel:description>Repository archive</rel:description><rel:inter_work_relation relationship-type="isSupplementedBy" identifier-type="doi">$repository_doi$</rel:inter_work_relation></rel:related_item>
           $endif$
+          $if(include_data_doi)$
           <rel:related_item><rel:description>Dataset archive</rel:description><rel:inter_work_relation relationship-type="isSupplementedBy" identifier-type="doi">$data_doi$</rel:inter_work_relation></rel:related_item>
+          $endif$
+          $if(include_book_doi)$
           <rel:related_item><rel:description>Book archive</rel:description><rel:inter_work_relation relationship-type="isSupplementedBy" identifier-type="doi">$book_doi$</rel:inter_work_relation></rel:related_item>
+          $endif$
+          $if(include_docker_doi)$
           <rel:related_item><rel:description>Container archive</rel:description><rel:inter_work_relation relationship-type="isSupplementedBy" identifier-type="doi">$docker_doi$</rel:inter_work_relation></rel:related_item>
+          $endif$
+          $if(include_software_review)$
           <rel:related_item><rel:description>GitHub technical screening</rel:description><rel:inter_work_relation relationship-type="isSupplementedBy" identifier-type="uri">$software_review_url$</rel:inter_work_relation></rel:related_item>
+          $endif$
+          $if(include_book_exec)$
           <rel:related_item><rel:description>Executable preprint</rel:description><rel:inter_work_relation relationship-type="isSupplementedBy" identifier-type="uri">$book_exec_url$</rel:inter_work_relation></rel:related_item>
+          $endif$
         </rel:program>
         <doi_data>
           <doi>$article.doi$</doi>