Recently, I have received the following warning when starting the program:
"You have preference sets with same definition, this might not work correct."
How to fix this problem? If possible without losing the current settings. Could it be because I recently went to a Dark Color theme mode?

Dark mode should not affect this. Can you go to Help > Support Info and send me the text from the Info tab page?

Here is the information you want. Hope this is helpful

PL/SQL Developer
Version 15.0.0.2043 Beta (64 bit)
Theme: Midnight Express / Office2019Black
Windows 10 Build 19043
de-DE(1031)/Deutsch (Deutschland)

Physical memory : 4.193.780 kB (615.384 available)
Paging file : 6.265.220 kB (1.153.420 available)
Virtual memory : 137.438.953.344 kB (137.434.083.956 available)

Parameters
E:\prg\db\tools\plsd15\plsqldev.exe

Preferences
Session mode: Dual
OCI Library: <none>
Use OCI7: False
Allow Multiple Connections: False

Preference Files
E:\prg\db\tools\plsd15\Preferences\Default\Default.ini
C:\Users\frankg\AppData\Roaming\PLSQL Developer 15\Preferences\frankg\default.dark.ini
C:\Users\frankg\AppData\Roaming\PLSQL Developer 15\Preferences\frankg\default.ini
C:\Users\frankg\AppData\Roaming\PLSQL Developer 15\Preferences\frankg\New.ini

Debug file
E:\prg\db\tools\plsd15\PlSqlDev.elf

Plug-Ins
*Active Query Builder (E:\prg\db\tools\plsd15\PlugIns\ActiveQueryBuilder.dll)
*PL/SQL Documentation (plsqldoc) (E:\prg\db\tools\plsd15\PlugIns\plsqldoc.dll)
(* is Active)

Aliases
adbfg1_high
adbfg1_low
adbfg1_medium
adbfg1_tp
adbfg1_tpurgent
...

Homes
OraClient19Home1 (E:\oracle\product\19.0.0\dbhome_1)

DLLs
E:\oracle\product\19.0.0\dbhome_1\bin\oci.dll

TNS File
E:\Oracle\product\19.0.0\dbhome_1\network\admin\tnsnames.ora

Using
Home: OraClient19Home1
DLL: E:\oracle\product\19.0.0\dbhome_1\bin\oci.dll
OCI: version 12.1 (19.3.0.0.0)
Oracle Database 19c Standard Edition 2 Release 19.0.0.0.0

Character Sets
Character size: 4 byte(s)
CharSetID: 873
NCharSetID: 2000
Unicode Support: True
NLS_LANG: GERMAN_GERMANY.WE8MSWIN1252
NLS_NCHAR_CHARACTERSET: AL16UTF16
NLS_CHARACTERSET: AL32UTF8

Process
Working Set = 166.154.240
Memory = 35.442.136
GDI Objects = 745
User Objects = 861
Handles = 765

Monitor
PixelsPerInch = 168

Id = 0
PPI = 168
Primary = True
Handle = 65537
Left = 0
Top = 0
Width = 2876
Height = 2037

MainFormOnTaskbar = True

Thanks. I see that you have created 2 additional preference sets:

default.dark.ini
New.ini

You will need to remove them or assign them to a specific connection. Go to the Preferences screen and click on the "Configure preference sets" button [...] to do so.