adverb
BAD : We finally got to see the secretary who confirmed that there was effectively a young man being held in prison.
GOOD : We finally got to see the secretary who confirmed that there was indeed a young man being held in prison.
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Effectively is used to show that you are describing what a particular situation is really like, especially when this is not obvious: 'At that time, free elections in Zambia were unknown, and Kaunda had, effectively, made himself life-president.'
Indeed is used to confirm that something is true, especially something that a person suspects but is unsure about: 'I imagined that Rupert had gone back to the hotel and indeed it was there that I found him, splashing around in the pool.'