How to switch an Application between Themed and not Themed at run-time?

Just for complement the Rob Kennedy answer, you must use the SetThemeAppProperties in this way.

uses
 UxTheme;

procedure DisableThemesApp;
begin
  SetThemeAppProperties(0);
  SendMessage(Application.Handle,WM_THEMECHANGED,0,0);
  SendMessage(Application.MainForm.Handle,CM_RECREATEWND,0,0);
end;

procedure EnableThemesApp;
begin
  SetThemeAppProperties(STAP_ALLOW_NONCLIENT or STAP_ALLOW_CONTROLS or STAP_ALLOW_WEBCONTENT);
  SendMessage(Application.Handle,WM_THEMECHANGED,0,0);
  SendMessage(Application.MainForm.Handle,CM_RECREATEWND,0,0);
end;

and to determine if your controls are themed or not you can use the GetThemeAppProperties function.

var
  Flag : DWORD;
begin
  Flag:=GetThemeAppProperties;
  if (Flag and STAP_ALLOW_CONTROLS)<>0 then //if the controls are themed
  begin

  end;
end;

UPDATE

Due to the issues described for you , i check the code of the UxTheme unit and i see the problem is related to the UseThemes function . so i wrote this small patch (using the functions to patch HookProc, UnHookProc and GetActualAddr developed by Andreas Hausladen), which works ok on my tests. let my know if works for you too.

you must include the PatchUxTheme in your uses list. and call the functions DisableThemesApp and EnableThemesApp.

unit PatchUxTheme;

interface


procedure EnableThemesApp;
procedure DisableThemesApp;


implementation

uses
Controls,
Forms,
Messages,
UxTheme,
Sysutils,
Windows;

type
  TJumpOfs = Integer;
  PPointer = ^Pointer;

  PXRedirCode = ^TXRedirCode;
  TXRedirCode = packed record
    Jump: Byte;
    Offset: TJumpOfs;
  end;

  PAbsoluteIndirectJmp = ^TAbsoluteIndirectJmp;
  TAbsoluteIndirectJmp = packed record
    OpCode: Word;
    Addr: PPointer;
  end;

var
 UseThemesBackup: TXRedirCode;

function GetActualAddr(Proc: Pointer): Pointer;
begin
  if Proc <> nil then
  begin
    if (Win32Platform = VER_PLATFORM_WIN32_NT) and (PAbsoluteIndirectJmp(Proc).OpCode = $25FF) then
      Result := PAbsoluteIndirectJmp(Proc).Addr^
    else
      Result := Proc;
  end
  else
    Result := nil;
end;


procedure HookProc(Proc, Dest: Pointer; var BackupCode: TXRedirCode);
var
  n: DWORD;
  Code: TXRedirCode;
begin
  Proc := GetActualAddr(Proc);
  Assert(Proc <> nil);
  if ReadProcessMemory(GetCurrentProcess, Proc, @BackupCode, SizeOf(BackupCode), n) then
  begin
    Code.Jump := $E9;
    Code.Offset := PAnsiChar(Dest) - PAnsiChar(Proc) - SizeOf(Code);
    WriteProcessMemory(GetCurrentProcess, Proc, @Code, SizeOf(Code), n);
  end;
end;

procedure UnhookProc(Proc: Pointer; var BackupCode: TXRedirCode);
var
  n: Cardinal;
begin
  if (BackupCode.Jump <> 0) and (Proc <> nil) then
  begin
    Proc := GetActualAddr(Proc);
    Assert(Proc <> nil);
    WriteProcessMemory(GetCurrentProcess, Proc, @BackupCode, SizeOf(BackupCode), n);
    BackupCode.Jump := 0;
  end;
end;

function UseThemesH:Boolean;
Var
 Flag : DWORD;
begin
  Flag:=GetThemeAppProperties;
  if ( (@IsAppThemed<>nil) and (@IsThemeActive<>nil) ) then
    Result := IsAppThemed and IsThemeActive and ((Flag and STAP_ALLOW_CONTROLS)<>0)
  else
    Result := False;
end;

procedure HookUseThemes;
begin
  HookProc(@UxTheme.UseThemes, @UseThemesH, UseThemesBackup);
end;

procedure UnHookUseThemes;
begin
  UnhookProc(@UxTheme.UseThemes, UseThemesBackup);
end;


Procedure DisableThemesApp;
begin
  SetThemeAppProperties(0);
  SendMessage(Application.Handle,WM_THEMECHANGED,0,0);
  SendMessage(Application.MainForm.Handle,CM_RECREATEWND,0,0);
end;

Procedure EnableThemesApp;
begin
  SetThemeAppProperties(STAP_ALLOW_NONCLIENT or STAP_ALLOW_CONTROLS or STAP_ALLOW_WEBCONTENT);
  SendMessage(Application.Handle,WM_THEMECHANGED,0,0);
  SendMessage(Application.MainForm.Handle,CM_RECREATEWND,0,0);
end;

initialization
 HookUseThemes;
finalization
 UnHookUseThemes;
end.

For one of my projects I used something like this:

Procedure RemoveTheme(Const Controls : Array Of HWnd; Const Redraw : Boolean = True);
Var
  I : Integer;
Begin
  If IsAppThemed And IsThemeActive Then Try
    I := 0;
    While (I < Length(Controls)) Do Begin
      If (Controls[I] > 0) And IsWindow(Controls[I]) Then SetWindowTheme(Controls[I], '', '');
      If Redraw Then Begin
        InvalidateRect(Controls[I], Nil, True);
        UpdateWindow(Controls[I]);
      End;
      Inc(I);
    End;
  Except
  End;
End;

Use like: RemoveTheme([Edit1.Handle, Edit2.Handle]);

Call SetThemeAppProperties.