This answer from Trevor gives a pretty good over all philosophy, but I want to get more at the details.
First, figure out why the alternate records are not being kept. This likely started out as either a foresight issue or a storage (paper or computer) issue.
At one time in the past, someone thought that the alternates would not be useful, so they were thrown out or deleted. This is likely a company culture problem. Now that this has been identified as an issue, it can be raised company-wide. Keeping records that have already been created is easy.
Even if the original engineers thought that the alternatives might be useful, they might have not kept the documents because of the cost of storage (physical or computer). If this is still the case, this problem needs to be resolved now. If this is no longer the case, the word needs to be spread throughout the company that keeping records is not a costly proposition.
Second, look at the alternative comparison method. There are two categories of alternative consideration: thought and calculation.
The thought comparisons are ideas that discarded quick enough that they never make it to paper in anything other than concept form. If these ideas were discarded so quickly the first time, then they probably don't need to be recorded. The effort to discredit them is so trivial that they will just be discredited again.
The alternatives that actually made it to the calculation stage should be kept in some form. If calculations or plans were done the first time, then there is already something to save. Even if the idea proves to be a dead-end, the work has already been done, so put it in the file! As long as it is dated, it can be referenced.
Write a memo (to the file if not to someone in particular) when a decision is made. This saves time in the future, but it adds a step to the process. This is something to work on along with improved documenting in general.
Last, date everything! Try to work with the systems that are already in place to keep the final records, just add a date to everything. Even if other methods of organization fail, the order of alternatives can be rebuilt using the dates on the items.