The Application Express Installation Guide and Release Notes provide you with information on Changed Behavior, Deprecated Features and Desupported Features. You can use this information to determine which parts of your applications need changes to work correctly with the new Apex version.

While these documents provide some clues and queries on how to find all the parts that need attention, actually finding them is quite a lot of work.
I created some queries that made my life easier; you can find these below together with the parts of the documentation I found useful. Not complete by any means, but maybe it is of some use.

Application Express Release Notes 21.1
Application Express Release Notes 21.2
Application Express Release Notes 22.1
Application Express Release Notes 22.2
Application Express Release Notes 23.1
Other Findings

https://docs.oracle.com/en/database/oracle/application-express/21.1/htmrn/index.html#GUID-657FF369-756E-4F31-96F9-B2D92C3DE084

5.1 Deprecated Features

5.1.1 Component View Tab Deprecated

5.1.2 Syntax {COLUMN_NAME}_LABEL in Interactive Grid Icon and Detail Views Deprecated

5.1.3 Date Picker (jQuery) Deprecated

5.1.4 Based On - Output of PL/SQL Code attribute Deprecated

7.1 Desupported Features

7.1.1 Websheets Desupported

7.1.2 Migration Workbench Desupported

7.1.3 REST Administration Interface Desupported

7.1.4 AnyChart, AnyMap, and AnyGantt charts Desupported

7.1.5 Productivity and Sample Applications Desupported

7.1.6 WWV_FLOW_EPG_INCLUDE_LOCAL for Web Entry Points Desupported

7.1.7 Download Interactive Report as RTF Desupported

7.1.8 History Table in Quick SQL Desupported

7.1.9 afterModify is Desupported

7.1.10 apex.page.confirm pMessage Parameter is Desupported

7.1.11 apex.navigation.dialog.fireCloseHandler function is Desupported

https://docs.oracle.com/en/database/oracle/application-express/21.2/htmrn/index.html#HTMRN-GUID-657FF369-756E-4F31-96F9-B2D92C3DE084

5.1 Deprecated Features

5.1.1 Deprecated Page Positions

I changed these with a search-and-replace in an application export file.
Took only 3 minutes and worked perfectly (which saved a lot time, there were 189 hits in my application...) select r.page_id , r.display_sequence , r.region_name , r.display_position_code from apex_application_page_regions r where r.display_position_code in ('BODY_1', 'BODY_2', 'BODY_3','AFTER_HEADER','BEFORE_HEADER') and r.parent_region_id is null -- excluded because these will be moved with their parent order by 1,2

5.1.2 Deprecated Region Positions

select b.page_id , b.region , b.button_sequence , b.button_name , b.display_position from apex_application_page_buttons b where b.display_position in ('TOP', 'BOTTOM', 'ABOVE_BOX', 'BELOW_BOX') order by 1,2,3

5.1.4 Legacy Substitution Strings Deprecated

These can be found by searching in the application itself, but I changed these with a couple of search-and-replace actions in an application export file.

https://docs.oracle.com/en/database/oracle/apex/22.1/htmrn/index.html#GUID-657FF369-756E-4F31-96F9-B2D92C3DE084

6.1 Deprecated Features

6.1.1 Deprecated APIs

6.1.2 Deprecated JavaScript APIs

6.1.3 Deprecated Attributes in App Builder

6.1.4 Deprecated Utilities

6.1.5 Deprecated Legacy Web Service References

6.1.6 Deprecated Properties

6.1.7 Deprecated View Columns

6.1.8 CKEditor4 Deprecation

8.1 Desupported Features

8.1.1 Desupported Page Positions

8.1.2 Desupported Region Positions

8.1.3 Custom Page Region Templates with Duplicated Positions Desupported

8.1.4 Legacy Substitution Strings Desupported

8.1.5 Desupported JavaScript Functions

8.1.6 Post Calculation for Page Items Desupported

8.1.7 Show / Hide All Page Items On Same Line Attributes Desupported

8.1.8 apex.server Plug-in and Process Function Async Option Desupported

8.1.9 apex.widget.initPageItem Function Desupported

8.1.10 Popup LOV Template Desupported

8.1.11 Based On - Output of PL/SQL Code attribute Desupported

8.1.12 Date Picker (jQuery) Desupported

8.1.13 Syntax {COLUMN_NAME}_LABEL in Interactive Grid Icon and Detail Views Desupported

8.1.14 Removed Content Delivery Network

8.1.15 APEX-Based REST Services Desupported

https://docs.oracle.com/en/database/oracle/apex/22.2/htmrn/deprecated-features.html#GUID-657FF369-756E-4F31-96F9-B2D92C3DE084

6 Deprecated Features

6.1 Deprecated Query Builder

6.2 Deprecated APEX Item Markup

6.3 Deprecated User Interfaces Removed

6.4 Deprecated APIs and Parameters

6.5 Deprecated jQuery/JET Date Pickers

8 Desupported Features

8.1 Desupported Attributes in App Builder

8.2 Desupported Properties

8.3 Desupported View Columns

8.4 FullCalendar 3 Desupported

8.5 App Builder Defaults Desupported

8.6 Copying Legacy Themes Desupported

8.7 CKEditor4 Desupported

8.8 Desupported Public Package APIs

https://docs.oracle.com/en/database/oracle/apex/23.1/htmrn/deprecated-features.html#GUID-657FF369-756E-4F31-96F9-B2D92C3DE084

5 Deprecated Features

5.1 CKEditor5 Deprecated

5.2 Deprecated Object Browser Features

5.3 Preventing Double Escaping of LOV Display Values

5.4 Display Only Item with Format HTML (Unsafe) Deprecated

5.5 Deprecated Functions and Procedures

7 Desupported Features

7.1 Desupported Query Builder

7.2 Desupported User Interfaces Removed

7.3 Desupported JET Date Picker Item Type Migrated

7.4 DOM Object Desupported

7.5 Legacy Bulk Utilities Desupported

Other things that needed attention during the upgrade:

• Somewhere between 20.2 and 23.1, view apex_application_page_rpt changed.
  In 20.2 it only showed Classic Reports, in 23.1 is also shows Interactive Reports.
  So, doing something like this for a page with both a Classic and an Interactive Report, you now get 2 results instead of 1: select reg.* from apex_application_page_rpt rpt join apex_application_page_regions reg on reg.region_id = rpt.region_id where rpt.application_id = p_app_id and rpt.page_id = p_page_id; I could not find any reference to this view in the release notes, so this was a bit of a surprise...