You can always clean up your TM on a regular basis, to ensure that it's most relevant and accurate.
If you cannot avoid sending the strings that don't need to be translated to Transifex, you can tag them as “Locked”, so translators won't be able to translate them:
find all the strings with the key "_notrans"
assign the 'locked" tag to them
You can tag the strings in the Editor, one by one, in bulk (filtering by Key), or via API.
If the file format is .xliff, .po, .xml, and the translation files are pulled from Transifex using the mode "sourceastranslation", the files will include the translated strings. The untranslated ones will be filled with the corresponding source strings.
However, if the resources are in the .plist or .string file format, then the default mode will work (download translation files for use).