It depends on your exact data and task.
In text processing one often has to deal with “missing” words, i.e., words that are not available in the index (e.g., rare words, typos, named entities). Such missing words are generally represented by a special word or token. For example, “the loudd noise woke me up” becomes “the  noise woke me up”. Maybe such a special “not available” token/value works for you as well.
Alternatively, is it a problem if the sequence is simply shorter. RNNs can handle sequences of different lengths.