The easiest thing to do is to return all the existing values in the database and build up a hash list.
// I guessed that it is an int, change it accordingly
var tableOneLookup = new HashSet<int>(Context.TAB_One.Id.Select(x => x.Id));
var tableTwoLookup = new HashSet<int>(Context.TAB_Two.Id.Select(x => x.Id));
// example of checking (check based on code you had shown before)
var modelsNotInTabOne = Models.Where(model => !tableOneLookup.Contains(model.RefIdOne)).ToList();
var modelsNotInTabTwo = Models.Where(model => !tableOneLookup.Contains(model.Id)).ToList();
// now do something with the results like create entity instances
If you are using strings as an identifier then you should add a string comparer. If you use StringComparer.OrdinalIgnoreCase it will ensure that case is NOT accounted for, pick the correct one you need.
new HashSet<int>(Context.TAB_Two.Id.Select(x => x.Id), StringComparer.OrdinalIgnoreCase);
Option 2
If your table has a massive number of records then the above solution is no longer performant. You could do the inverse by finding which ids are in the database and then filter on that result.
// create lists of just the ids
var modelOneIds = Models.Select(model => model.RefIdOne).ToList();
var modelTwoIds = Models.Select(model => model.Id).ToList();
// create a list of ids found in the db
var foundInTableOne = new List<int>();
var foundInTableTwo = new List<int>();
// iterate over the model in batches of 1000, the translated IN clause in Sql has a limit. You can tweak this number accordingly
const int batchSize = 1000;
for(int i = 0; i < Models.Count; i+=batchSize){
var tmpModelOneIds = modelOneIds.Skip(i).Take(batchSize).ToList();
var tmpModelTwoIds = modelTwoIds.Skip(i).Take(batchSize).ToList();
foundInTableOne.AddRange(Context.TAB_One.Where(itm => tmpModelOneIds.Contains(itm.Id)).Select(itm => itm.Id));
foundInTableTwo.AddRange(Context.TAB_Two.Where(itm => tmpModelTwoIds.Contains(itm.Id)).Select(itm => itm.Id));
}
// find the models not found in the DB
var modelsNotInTabOne = Models.Where(model => !foundInTableOne.Contains(model.RefIdOne)).ToList();
var modelsNotInTabTwo = Models.Where(model => !foundInTableTwo.Contains(model.Id)).ToList();
// now do something with the results like create entity instances