There may be a style file which you usually do not need to edit. You may use other text editors to do this, but Emeditor is very good in editing very large text files.
Use MdxBuilder to compile the content text file back to mdx.
If the content file use compact Html (a unique Mdict format), you will need to specify the style file for the compiler as well. Otherwise you will only need to tell the compiler where the content text file is.
If you are not using Windows, you may use Mdict-utils, which are available on Windows, Unix and Mac. See post 1 or post 14 for links to download Mdict-utils.
Sone users have reported, that Mdict-utils can only decompile Unicode 8 files without signatures, and will not be able to extract style files for compact Html.
In that case, you may also try using a Windows Virtual machine, which has been discussed in this post.
I finally found the root of the problem: one of the text files I merged was incorrectly saved as 'UTF-8 with Signature". I changed to ‘without Signature’ and the MDX was properly built with no errors to the index.