The plugin CJ Disabled Shortcut can be used to disable clipjump when pressing shortcuts like Clip Note in CintaNotes and similar features in Evernote, OneNote and other note-taking applications.
Basically this plugin disables clipjump around the span of pressing a shortcut which alters clipboard and thus puts unneeded entries to Clipjump.

To use this plugin, you will have to set a separate ClipjumpCustom binding for the shortcut you want to disable clipjump for. Here I will take example of CintaNotes and its Clip Text Hotkey (Ctrl+F12) shortcut.
After downloading the above plugin, put this code in ClipjumpCustom.ini .

[cintanotes_clip_text]
bind = Win + F12

run = API.runPlugin(cjdisabledShortcut.ahk, Ctrl+F12, 1200)

The CJdisabledShortcut plugin has two parameters.

  1. The shortcut_key - The key for which you want Clipjump blocked for. Here “Ctrl+F12”
  2. The delay - The delay between pressing the “blocked shortcut” and re-enabling Clipjump. Here “1200”

The bind key sets up “Win + F12” as the shortcut for this process. Now you can press Win + F12 to duplicate the feature of Ctrl+F12 without invoking Clipjump.
Same can be done for other applications.
One good idea will be to change the CintaNotes Ctrl+F12 shortcut to something un-usable like Ctrl+Alt+Shift+F12 so that you don’t waste a usable shortcut space. This is just a suggestion, just what I have done here with the clipping shortcuts of CintaNotes and Evernote.

Update

Well, you can do this with ClipjumpCustom alone, no need to use a plugin -

[cn_clip_text]
bind = win + f12

run = API.blockMonitoring(1)

zsomevar = %HParse(Ctrl+F12, 1, 1, 1)%

send = %zsomevar%

sleep = 1200

run = API.blockMonitoring(0)

Please ask if you face problems..