You can always create one huge opening in cpt and import all of your repertoire pgn games. And train you complete repertoire this way.
Chess Position Trainer in Conjunction with Chessbase or Similar
I tried all these. I have my repertoire in all 3 and take it to chesstempo mainly just to visually assess the branches in tweaking it in effort of trying to take my total unique positions needed to learn down.
In chess position trainer I put "Tournament" as the repertoire. And then under the folder as Black, I put Xopening Minor Lines as its own opening and then I put 7 variations and three 3 sub variation book mark names for it (similar to chesstempo with bookmarks). One variation might have 20 or more lines for example.
I'm pretty sure you can go systematically and randomly through each entire opening. You can be as specific as possible in the training - when you have the training stage open which shows a start button, there will be an element on left for navigation, right of that is move list, and right of that is "Opening to train: " above the chess board. Opening train is the drop down menu so you could click any of the stages like repertoire or the black folder, or an opening or a variation bookmark you made.
If I wanted to add something late, I'd probably delete things manually from x move and then import it. I'm not aware how easy CPT can export, so I think changes may need to occur in chessbase/chesstempo instead and then one sided brought back to CPT. I'm still a beginner though with it, I find their spaced repetition less appealing to systematic personally.

If you are saying you have your repertoires in Chessbase. What do you mean? You have uploaded them online to my-moves? Or just that you have them in cbh format and set them as your white and black repertoires when right clicking the databases.
I have tried my-moves of Chessbase and find it verry confusing and not user friendly.
I like Chess Position Trainer, to bad it is buggy sometimes, and there where no updates anymore in latest years.
You can select a folder and train all openings in this folder, but the option to show eco code and opening names doesn't work in that case for some reason.
I like the scheduled training in cpt, and I think it is unique for cpt. Chessable and Chesstempo also has some sort of spaced repetition, but not like cpt.
With cpt you get a weekly training schedule. If I stick to it, I think I will improve my chess.
I use it for openings, tactics and endgames.
I have a repertoire stored in Chessbase and currently export these as PGNs when updated, and train them in ChessTempo for its spaced repetition. I do not like the Chessbase repertoire training feature, as it doesn't let me go through my entire repertoire.
Enter Chess Position Trainer. I am battling through the manual during the evaluation period. My questions are:
a) can you train your entire repertoire in one swoop? Or are you forced to choose each opening module and train one at a time? I am thinking along the lines of ChessTempo's white/black repertoire with spaced repetition.
b) does anyone have a decent workflow for exporting Chessbase repertoires and importing them into CPT? If I make small adjustments in Chessbase, how much destruction will I cause to my current CPT repertoire my importing that new PGN? I understand that it will add new positions, but will it delete old unused ones?
Many thanks in advance.