I am assuming you are using GNome.
If you are reporting that the application is disappearing from your 'Favourite' bar, it maybe due to the item not being added to gnome favourite bar.
Step 1 :
Make sure you create a .desktop file with the appropriate exe/icon :
[ECLIPSE]
Name=Eclipse
Exec=/absolute/path/of/executable
StartupNotify=true
Terminal=false
Type=Application
Icon=/absolute/path/of/png
Step 2 : You can use this to get the current list :
gsettings get org.gnome.shell favorite-apps
Step 3 : Depending on your need, copy the desktop file to either
/usr/share/applications/(if you need this available for other users) or ~/.local/share/applications(if you need this available only for your user).
Step 4 : Get the current favourite apps :
gsettings get org.gnome.shell favorite-apps
Step 5 : Add the new app into the favourite app list. Here is an example :
gsettings set org.gnome.shell favorite-apps "['firefox.desktop', 'Terminal.desktop', 'Eclipse.desktop', 'EMACS.desktop']"