Can consuming a protein shake in the morning as a meal replacement affect the effect of certain medications?

Yes, the absorption of some drugs could be affected, but it would be necessary to specify which drug exactly. For example, levodopa used in Parkinson's disease competes with proteins for absorption. In more advanced Parkinson's disease, this could be significant. If the shake also contains calcium, magnesium or iron in the "vitamin" part, it may interfere with the absorption of some medications, e.g. synthroid. However, it is only a few specific drugs that are affected, for most there will be no problem. It is therefore necessary to check specifically for the medication you are taking.