Don't use String#replaceAll in this case if there is slight chance part you will replace your string contains substring that you will want to replace later, like "distance" contains a and if you will want to replace a later with "velocity" you will end up with "disvelocityance".
It can be same problem as if you would like to replace A with B and B with A. For this kind of text manipulation you can use appendReplacement and appendTail from Matcher class. Here is example
String input = "((a+b)/(c+(d*e)))";
Map<String, String> replacementsMap = new HashMap<>();
replacementsMap.put("a", "velocity");
replacementsMap.put("b", "distance");
replacementsMap.put("c", "time");
StringBuffer sb = new StringBuffer();
Pattern p = Pattern.compile("\\b(a|b|c)\\b");
Matcher m = p.matcher(input);
while (m.find())
    m.appendReplacement(sb, replacementsMap.get(m.group()));
m.appendTail(sb);
System.out.println(sb);
Output:
((velocity+distance)/(time+(d*e)))
This code will try to find each occurrence of a or b or c which isn't part of some word (it doesn't have any character before or after it - done with help of \b which represents word boundaries). appendReplacement is method which will append to StringBuffer text from last match (or from beginning if it is first match) but will replace found match with new word (I get replacement from Map). appendTail will put to StringBuilder text after last match.
Also to make this code more dynamic, regex should be generated automatically based on keys used in Map. You can use this code to do it
StringBuilder regexBuilder = new StringBuilder("\\b(");
for (String word:replacementsMap.keySet())
    regexBuilder.append(Pattern.quote(word)).append('|');
regexBuilder.deleteCharAt(regexBuilder.length()-1);//lets remove last "|"
regexBuilder.append(")\\b");
String regex = regexBuilder.toString();