Optimizing your website you always have to worry about being excluded from a search engine's index. The majors search engines use techniques to detect over optimized ethical SEO or SEO spam. It may happen that is acceptable for a search engine what it is over optimized for another one. For example Yahoo may appreciate a keyword density about 8% or 9% but Google may consider already too much 7%.
This is one of the reasons, for which is tricky to optimize for all the possible search engines.
Following only the suggestions of the first three chapters of this paper you will probably able to achieve good results with no risks. But if you need a special boost, you may use the SEO spam techniques or exaggerate with ethical optimization. This can sometimes lead to the nightmare of the SEO specialists: being excluded from the index of a search engine. So you will have the problem to be reenlisted in its index.
The first step to do is to analyse why it happened: it is useless to submit a reinclusion request when you did not change anything in your website, this might compromise the opportunity to be again in the index in the case the search engine keeps a statistics of the misbehaving websites. In this phase the webmaster guidelines, which are usually present in the help section of the search engines, can be useful to understand how you are supposed to behave.
Then you will have to send an email or fill a form with the reinclusion request. For instance, in the case you were excluded by the Google's index you have to fill the form at the address: http://www.google.com/support/bin/request.py. Filling the form you should try as much as possible to be polite and admit the errors you did.
Finally you will have to wait for an answer. It is a very poor idea to send more then a request for the same website until you will get the answer.