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That is one reason sequences are not usually the best choice for a program architecture. Dataflow can provide most of the "sequencing" that is required.
Simply removing the sequence will leave the dataflow connections intact. That may be all that is needed, if you are lucky. Then you can stretch the loop over the part you want inside the loop.
SubVIs may be a good choice for encapsulating related portions of the code.
Beyond that, without seeing the code it is difficult to recommend options.
If you need to split it in half and do not want to rewrite everything, try duplicating the entire sequence. Put the duplicate into the while loop. Delete the last half of one sequence and the first half of the other. If there are controls or indicators inside the sequence, they will get duplicated also and this can get messy.