i managed to solve this by clicking view > onion skin > onion skin by frames!
not sure why the setting suddenly changed for me, but that seemed to fix it for me!
I’m having the same problem in Harmony 20 Premium. I have it set to “Show Onion Skin” and “Onion Skin by Frames” is selected but the handles still don’t appear in the timeline. Somebody please help!
Found a fix for anyone who might encounter the same problem. In Edit > Preferences, I had “Flat Tool Toolbar” enabled under the General > Options tab. Make sure you uncheck that, restart the software and the problem should be gone.
It’s annoying as I prefer not to have my icons nested, but it will have to do until it the bug is fixed.
I know this is a very old thread, but this problem still exists. At least in the form that BobbyBaxter described above, where it is caused by using the Flat Tools Toolbar.
I believe I have found the fix:
Quit Harmony
Go to C:\Program Files (x86)\Toon Boom Animation\Toon Boom Harmony 22 Premium\resources (or the equivalent folder for your version of Harmony)
Open toolbars.xml in a text editor
Find the “// Drawing Tools ( Flat Version )” section
In that section, locate the following code:
<item
checkable="true"
icon="drawingtool/onionskin_show.png"
id="OnionSkinToggle"
responder="onionSkinResponder"
slot="onActionOnionSkinToggle()"
text="Show Onion Skin"
tooltip="Mode for displaying previous and/or following 
drawings (or frames) for judging movement progression."/>
In the 6th line shown above, add “BaseMode” exactly as shown below in bold:
slot=“onActionOnionSkinToggleBaseMode()”
Restart Harmony
The Toggle Onion Skin button will now not only toggle the onion skin, but will force it to the non-advanced mode. (The non-flat toolbar version of this button already has the “BaseMode” bit, but Toon Boom seem to have forgotten to include it in the flat toolbar version of the button).
If you use this button on other toolbars (eg. the Camera View toolbar) you can perform the same fix on those instances of the button by locating the onActionOnionSkinToggle() in the appropriate section in toolbars.xml and changing it to onActionOnionSkinToggleBaseMode(), just as above.