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Here is some SQL that does the job, including fixing the issuelinktype  if you hadn't already done so above.

Code Block
-- https://www.redradishtech.com/pages/viewpage.action?pageId=14483457
begin;
create temp sequence issuelink_seq start with 99999; -- https://stackoverflow.com/questions/37057643/postgresql-starting-a-sequence-at-maxthe-column1                                                                                        
select setval('issuelink_seq', (select max(id::bigint)+1 from issuelink));
WITH jpolinks AS (
	    select entity_id AS child_id, (json_value::json->>'parent_id')::numeric AS parent_id from entity_property where entity_name='IssueProperty' and property_key='jpo-issue-properties')                                                     
, newissuelinks AS (
  select nextval('issuelink_seq') AS id
		        , jpolinktype.id AS linktype
		        , parent_id AS source
		        , child_id as destination
		        ,  null::numeric AS sequence
  from jpolinks
    CROSS JOIN (select id from issuelinktype where linkname='Parent-Child Link') jpolinktype
  where parent_id is not null -- the parent_id JSON is sometimes empty
    and not exists (select * From issuelink where source=parent_id and destination=child_id and issuelinktypelinktype=jpolinktype.id) -- don't double-insert                                                                                              
)
insert into issuelink select * from newissuelinks;
update sequence_value_item set seq_id=nextval('issuelink_seq') where seq_name='IssueLink';
update issuelinktype set pstyle=null where pstyle='jira_jpos_parent_child'; 
commit;

After running the above, you will have to restart Jira for the changes to take effect.

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then when you disable Portfolio, the Child issues  section disappears, and you are where you want to be.

Addendum: post-uninstall log errors

After uninstalling Portfolio, you might find your atlassian-jira.log  file being filled with errors on each page load:

Code Block
2019-11-11 00:59:59,234 ajp-nio-127.0.0.100-8009-exec-4059 WARN jturner 59x3059696x3 56p7sr 10.36.2.100 /browse/CC-5353 [c.a.r.j.p.w.children.condition.ChildIssuesPanelVisibilityCondition] Exception when evaluating if child issues panel should be displayed.
com.atlassian.rm.common.env.EnvironmentPortfolio1NotAvailableException: com.atlassian.rm.common.bridges.api.plugins.PluginNotAvailableException
        at com.atlassian.rm.common.env.license.JiraLicenseService.getLicenseInformation(JiraLicenseService.java:36)
        at com.atlassian.rm.common.env.license.JiraLicenseService.isLicensed(JiraLicenseService.java:45)
        at com.atlassian.rm.jpo.plugin.webpanels.children.condition.ChildIssuesPanelVisibilityCondition.isLicensed(ChildIssuesPanelVisibilityCondition.java:81)
        at com.atlassian.rm.jpo.plugin.webpanels.children.condition.ChildIssuesPanelVisibilityCondition.shouldChildrenBeVisible(ChildIssuesPanelVisibilityCondition.java:68)        at com.atlassian.rm.jpo.plugin.webpanels.children.condition.ChildIssuesPanelVisibilityCondition.shouldDisplay(ChildIssuesPanelVisibilityCondition.java:54)
        at com.atlassian.plugin.web.DefaultWebInterfaceManager.filterFragmentsByCondition(DefaultWebInterfaceManager.java:154)
        at com.atlassian.plugin.web.DefaultWebInterfaceManager.getDisplayableWebPanelDescriptors(DefaultWebInterfaceManager.java:117)
        ... 2 filtered
        at java.lang.reflect.Method.invoke(Method.java:498) ...

In Jira's Manage apps  admin page you will find these two vestigial plugins:

Image Added

Uninstall them and your Jira should be back to normal. Jira's plugin system lets plugin authors package reusable parts as separate plugins, but isn't smart enough to uninstall them when the parent plugin is uninstalled.