In my opinion if you still have VALID Indian Passport and putting queries in installments I have now following to value add;
1. If whatever you are doing in Cyprus is finished / terminated then purchase flight ticket to come back to India and while leaving authorities there may question but then they will allow you to leave. However, you will not be allowed to re-enter Cyprus in future.
2. Once you comeback to Indian soils, invite your Croatian G/F to India and marry her as per Special Marriage Act (SMA) and REGISTER such marriage under SMA. Such a marriage is solemnized before the marriage officer / registrar usually D.C. Deputy Commissioner of the Area / SDM where both or any one of the parties to such a marriage reside permanently or for at least one month. Refer to some of my oldest post on Indian marrying foreigner in India for knowing details of procedure to marry under SMA.
3. After registering marriage under SMA here in Indian soils apply jointly IN-PERSON before then Croatian Embassy (acceding to EU) for flying with Croatian wife to next dream destination is spouse visa allowed by them!
If you still overstay there and marry in-between then previous reply will not be entertained by Indian High Commission in Nicosia.
Hope your two issues; expired residency + marriage is sorted with above addendum reply?
If you still have more stories in installments to spell out for legal opinion then welcome to do so in the forum, someone will reply. I for one don’t care if you are Lee or John or Rambo here until query has some legal opinion to give.