"They" can do either, especially if the charges are based on more than just the CI stuff, and they probably are. If they are only based on the CI stuff, they can STILL go with that, but the negative info is something that your attorney can use to support your case. Either way, get an attorney on this ASAP!
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All Confidential Informants have credibility issues, but that will not win the day for you. That is why most of their activity is monitored, or supported by other evidence.
RE: the "tampered" evidence - it depends on what you mean by "tampered with." It may still have evidentiary value, but that is for the prosecutor to decide. It sounds like your attorney may have a great deal to work with.
If you are far enough along in this process to know that the C.I. is back in jail AND to know that there is a problem with the meth found in your case, then I am sure you already have an attorney. You need to discuss this with them thoroughly, and place some trust in their response. If you can't trust your attorney and/or cannot work with them, consider getting a new one.
Bear in mind that the attorneys here - or on any other public forum - don't know the details of your case. You need to rely on your counsel.
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