Is a line break (line ending character) disappearing unexpectedly when you merge a document? For example, perhaps a line of text is automatically moving up to the end of the line of text that was above it. Or, vice-versa, a line of text is automatically moving down to the beginning of the line of text that was below it.

If a merge is removing a line break (line ending character), then the line ending character has most likely been included inside a variable text link. When a Line Ending character is included inside a variable text link, a merge will automatically remove that Line Ending character because incoming variable data will replace all of the characters that are inside the text link, including the Line Ending character.

There are several simple and easy ways to move a Line Ending character to the outside of a variable text link. For example, simply highlight/select the line ending character and nothing else, then click the Remove button on the DesignMerge panel (DesignMerge > View > DesignMerge Panel). Alternatively, highlight/select the line ending character and nothing else, then open the DesignMerge menu and choose Utilities > Link > Clear Selection Range. 

To confirm no line endings have been inadvertently included inside variable text links, place your text cursor inside the frame that contains the variable text links and then click the Previous (<<) or Next (>>) buttons on the DesignMerge panel to have DesignMerge select all of the text that is inside each variable link in the frame. 

Also, when entering text in a frame where variable text links have already been inserted, you will want to remember that InDesign will automatically include inside a variable text link any text that you enter immediately following a variable text link and also InDesign will automatically inside a variable text link any text that you enter immediately preceding a variable text link that is at the beginning of a line. 

To prevent line ending characters from being included inside new variable text link assignments, turn on the DesignMerge Smart Tags preference (open the DesignMerge menu and select Preferences to access this preference). When this preference is enabled, DesignMerge will automatically exclude non-printing characters, such as a Line Ending character, that are at the beginning or end of your selected text from being placed inside a new or replaced text link.