Hi Kari,
If I'm understanding your language data and the orthography correctly, the one "na" is linguistically a proclitic, but in the orthography it is treated as an enclitic (at least in the data you shared). To reflect both of those realities, your lexical entry will need to have an allomorph that is an enclitic (=na) if you choose to reflect the linguistic reality by making the lexeme form a proclitic
(na=). (Does your project use the equals sign to designate a clitic? I'm wondering because you used hyphens in your message instead of equal signs.)
A question about how the possessive suffix is written in the orthography: Is the hyphen part of the orthography, used to differentiate the possessive suffix (bola-na) from the pronominal clitic (tonna)? Or did you just put the hyphen in "bola-na" in your example to show that the "-na" is a suffix, but in the orthography, the word is written "bolana"? If the hyphen is part of the orthography, have you changed the affix-marking symbol to something else so that FLEx is not confused by the ambiguity?
FLEx knows the difference between a clitic and an affix, so assuming the possessive suffix and the pronominal clitic are both tagged appropriately, there should be two separate entries in the Word Analyses section of the Texts & Words area--one for -na (suffix) and another for na= (clitic). In each one, you can manually approve or disapprove the analyses that you do or do not want for it, and that will overrule any suggestions that FLEx might otherwise be inclined to make as you interlinearize. I've found this to be a good way to deal with one-of-a-kind elements in my lexicon.
Hope that helps,
Kevin