(notes on how to move back many dialogue entries at once after they’ve fallen to the bottom of the ocean by some glitch or other)

Install tes3cmd in the Data Files folder, backup your files, etc.;
use tes3cmd v0.37 (the modify function doesn't work in v0.40 alpha)
Set up command line calls with a batch (.bat) file is advised, or else call command line window on Data Files;
Make text dumps of vanilla & TR records so you can look up IDs in them when necessary (attached);
Make text dump of the plugin you’re fixing, likewise,
Taking the example of “background” entries in the Indoril-Thirr merge:

tes3cmd dump --type DIAL --type INFO "TR_IndorilThirr_v.0110.esp" > "IndorilThirr_Dial.txt"

Look up the entry above which you want to move dialogue in the topic – can be in vanilla or TR. For this example let’s assume we’re moving these entries just above the top entry in Tribunal:

We’ll need the ID of this one: 2583529070786213408,

Look up the top and bottom of the entries you want to move in the plugin dump:

in this case we’ll respectively delete (replace with nothing) the Prev_ID (=666731499111789993) of the top one so nothing is above it (if it needs to be placed somewhere specific, find the ID that goes above instead), and replace (since there is nothing, add with the character ^) the bottom’s Next_ID (empty) with the ID of the top Tribunal entry so it ends up positioned above it:

tes3cmd modify --type info --exact-id "20552131232024725953" --sub-match "Prev_id:" --replace "/666731499111789993//" TR_IndorilThirr_v.0110.esp
&
tes3cmd modify --type info --exact-id "18859804930419111" --sub-match "Next_id:" --replace "/^/2583529070786213408/" TR_IndorilThirr_v.0110.esp

Restricting to info-type and to the precise id of the entry to be modified is a necessary precaution;
Restricting to sub-match "Next_id:" or sub-match "Prev_id:" is the only way to replace an empty field.

And check in the CS.

ADDENDUM:
obviously typing strings is more error-prone than editing in the CS so use .bat files in which you paste the tes3cmd command lines so you don't have to type these long IDs.
Still better to prevent the reference loss from happening when merging plugins in the first place. Always make sure that newly merged entries are not placed at the very top, or very bottom, of the dialogue list for Greetings and common topics because these positions deprive your added entries of an upper (resp. lower) reference. If entries only have a lower reference they have twice the chances of dropping after merges not true: the "previous" reference is the only one that counts, and "nothing" counts as a legitimate previous reference. What doesn't count as a previous reference is an ID that isn't found, and that's when dialogue falls to the bottom. So placing dialogue at the very top is technically safer, and the old wisdom was wrong.