Retrofit by design has to rely on the same structure within the documents so it can reliably bring back the (small) review changes to the bilingual document. When changes become too significant, it is better to fall back on more manual updates to the document and TM, or even consider (re-)alignment after the project has finished to get the final segment pairs into the TM.
Retrofit performance could be better if it was possible to improve results in the alignment view.
At present, it is possible to align segments within the same parapgraph. It should be possible to manually align segments of the entire text without limits as in the regular alignment function.
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