It looks like a new gamma has been released which addresses this exact issue. It also allows "snapshots" which are basically backups of your mudlet files, similar to a snapshot of a virtual machine.
http://www.mudlet.org/2015/01/mudlet-3-0-0-gamma-preview-3/Mudlet 3.0.0 gamma! (preview #3)
January 6th, 2015
This third preview release of Mudlet 3.0 fixes an important issue from the beta – one where the content of an alias/trigger/script could be wiped depending on the way you’ve navigated.
In this version, we only focused on fixing new issues have have been introduced in 3.0 – such that 3.0 is no worse, only better, than 2.1 quality-wise. It is also, of course, better feature-wise
Please provide all feedback (don’t delay!) on our forums.
Documentation has been updated for all new features.
Below is the summary of changes in preview #3. See preview #1 and #2 for a list of all the new things in 3.0!
Script content loss
An issue not present in 2.1 but introduced in the 3.0.0 beta was one where depending on the way you navitated the editor, the content of an alias, trigger or script could be wiped. This has been rectified. You can also use the snapshots feature of Mudlet to restore any lost data by selecting to load an older profile.
sendMSDP() fixed
sendMSDP() has been fixed to allow a variable number of variables.
Double-click word selection
Double-click to select a word has been fixed to stop selecting to the left of selection, and the settings window has been fixed to to store the settings for double-click characters properly.
Documentation
Documentation on wiki.mudlet.org has been combed through and updated for all new features present in the upcoming Mudlet 3.0.
Outstanding issues
There are just a few issues outstanding in order to make the 3.0 final release happen. If you spot any new issues that came since 2.1, please let us know about them!