My guess is that your work permit won't interfer with the ancestry visa, but this is something that only an immigration lawyer would be qualified to advise you on. In many cases you may need to leave the country to apply for the visa, so it would be easier to just sort out the right visa before you leave home.
I would talk to your employer about letting you get the ancestry visa - it will save them paperwork and you have a more flexible visa that will let you stay in the UK.
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